Diversity of sequence types and impact of fitness cost among carbapenem-resistant Acinetobacter baumannii isolates from Tripoli, Libya

We investigated the molecular epidemiology of 21 carbapenem-resistant A. baumannii from Libya, and assessed their relative fitness. Core-genome MLST revealed five inter-hospital transmission clusters. Three clusters were associated with the international clones (IC) IC1, IC2, and IC7. Carbapenem-resistance was associated with bla OXA-23, bla GES-11 , or bla NDM-1 . Compared to A. baumannii DSM 30008, the doubling time was similar over 10 hours, but after 16 hours, half the isolates grew to higher densities, suggesting a fitness advantage.

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Diversity of Oxacillinases and Sequence Types in Carbapenem-Resistant Acinetobacter baumannii from Austria

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18042171 ◽

2021 ◽

Vol 18 (4) ◽

pp. 2171 ◽

Cited By ~ 1

Author(s):

Andrea Grisold ◽

Josefa Luxner ◽

Branka Bedenić ◽

Magda Diab-Elschahawi ◽

Michael Berktold ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Genetic Background ◽

Regional Differences ◽

Carbapenem Resistance ◽

Carbapenem Resistant ◽

Class D ◽

Acinetobacter Spp ◽

First Time ◽

Sequence Types ◽

Significant Health

Carbapenem-resistant Acinetobacter baumannii is a significant health problem worldwide. A multicenter study on A. baumannii was performed to investigate the molecular epidemiology and genetic background of carbapenem resistance of A. baumannii isolates collected from 2014–2017 in Austria. In total, 117 non-repetitive Acinetobacter spp. assigned to A. baumannii (n = 114) and A. pittii (n = 3) were collected from four centers in Austria. The isolates were uniformly resistant to piperacillin/tazobactam, ceftazidime, and carbapenems, and resistance to imipenem and meropenem was 97.4% and 98.2%, respectively. The most prominent OXA-types were OXA-58-like (46.5%) and OXA-23-like (41.2%), followed by OXA-24-like (10.5%), with notable regional differences. Carbapenem-hydrolyzing class D carbapenemases (CHDLs) were the only carbapenemases found in A.baumannii isolates in Austria since no metallo-β-lactamases (MBLs) nor KPC or GES carbapenemases were detected in any of the isolates. One-third of the isolates harbored multiple CHDLs. The population structure of A. baumannii isolates from Austria was found to be very diverse, while a total of twenty-three different sequence types (STs) were identified. The most frequent was ST195 found in 15.8%, followed by ST218 and ST231 equally found in 11.4% of isolates. Two new ST types, ST2025 and ST2026, were detected. In one A. pittii isolate, blaOXA-143-like was detected for the first time in Austria.

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Subtypes, resistance and virulence platforms in extended-drug resistant Acinetobacter baumannii Romanian isolates

Scientific Reports ◽

10.1038/s41598-021-92590-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Irina Gheorghe ◽

Ilda Czobor Barbu ◽

Marius Surleac ◽

Ionela Sârbu ◽

Laura Ioana Popa ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Carbapenem Resistance ◽

Control Measures ◽

Drug Resistant ◽

Infection Control Measures ◽

Carbapenem Resistant ◽

Ambulatory Patients ◽

Severe Infections ◽

Healthcare Associated ◽

Sequence Types

AbstractAcinetobacter baumannii has emerged worldwide as a dominant pathogen in a broad range of severe infections, raising an acute need for efficient antibacterials. This is the first report on the resistome and virulome of 33 extended drug-resistant and carbapenem-resistant A. baumannii (XDR CRAB) strains isolated from hospitalized and ambulatory patients in Bucharest, Romania. A total of 33 isolates were collected and analyzed using phenotypic antibiotic susceptibility and conjugation assays, PCR, whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE) and MultiLocus Sequence Typing (MLST). All isolates were extensively drug-resistant (XDR), being susceptible only to colistin. The carbapenem resistance was attributed by PCR mainly to blaOXA-24 and blaOXA-23 genes. PFGE followed by MLST analysis demonstrated the presence of nine pulsotypes and six sequence types. WGS of seven XDR CRAB isolates from healthcare-associated infections demonstrated the high diversity of resistance genes repertoire, as well as of mobile genetic elements, carrying ARGs for aminoglycosides, sulphonamides and macrolides. Our data will facilitate the understanding of resistance, virulence and transmission features of XDR AB isolates from Romanian patients and might be able to contribute to the implementation of appropriate infection control measures and to develop new molecules with innovative mechanisms of action, able to fight effectively against these bugs, for limiting the spread and decreasing the infection rate and mortality.

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Investigation of carbapenem resistant Acinetobacter baumannii ST2 in Iran

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2020.01164 ◽

2020 ◽

Author(s):

Aliakbar Rezaei ◽

Hossein Fazeli ◽

Jamshid Faghri

Keyword(s):

Acinetobacter Baumannii ◽

Clonal Complex ◽

Carbapenem Resistance ◽

Diffusion Method ◽

Disc Diffusion Method ◽

Carbapenem Resistant ◽

Rapd Pcr ◽

Relationship Of ◽

Sequence Types ◽

Respiratory Specimens

AbstractThis study investigated carbapenem resistance among Acinetobacter baumannii isolated from respiratory specimens. Epidemiological relationship of the isolates was also evaluated. In this study, 81 respiratory specimens of A. baumannii from AL Zahra Hospital were confirmed by phenotypic and genotypic methods. Antimicrobial susceptibility was performed by disc diffusion method. Carbapenem resistance genes were identified by PCR. The isolates were typed by RAPD-PCR and multilocus sequence typing (MLST) methods. All isolates were resistant to imipenem and 80 isolates to meropenem. Frequency of oxacillinase genes was as follows: blaOXA-23 gene was positive in 74 (91.3%), blaOXA-24 gene in 50 (61.7%) and blaOXA-58 was not found in any isolates. On the other hand 22 (27.2%) isolates contained blaIMP-1, 3 (3.7%) isolates contained blaIMP-2 gene, 5 (6.2%) isolates contained blaVIM-1, 4 (5%) isolates had blaVIM-2 and none of the isolates had blaSIM-1 gene. RAPD-PCR typing identified 16 different patterns, with one pattern being the most frequent one in 26 isolates. In MLST 6 different sequence types were identified, the most predominant being ST2 belonging to clonal complex 2. The results of this study showed high resistance to carbapenems as well as high abundance of oxacillinase genes.

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Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolated from War-Injured Patients from the Eastern Ukraine

Antibiotics ◽

10.3390/antibiotics9090579 ◽

2020 ◽

Vol 9 (9) ◽

pp. 579

Author(s):

Paul G. Higgins ◽

Ralf Matthias Hagen ◽

Andreas Podbielski ◽

Hagen Frickmann ◽

Philipp Warnke

Keyword(s):

Acinetobacter Baumannii ◽

Core Genome ◽

Acquired Resistance ◽

Sequence Type ◽

Carbapenem Resistant ◽

Next Generation Sequencing Ngs ◽

Injured Patients ◽

Sequence Types ◽

Generation Sequencing ◽

Epidemiological Information

Recently, a total of 32 carbapenem- and fluoroquinolone-resistant Acinetobacter baumannii (Ab) isolates was isolated from war-injured patients who were treated at German Bundeswehr Hospitals, and preliminarily typed by “DiversiLab” repetitive elements sequence-based (rep-) PCR. Core genome-based sequence typing was also used to provide more detailed epidemiological information. From the clusters observed by rep-PCR, selected Ab strains were subjected to Next Generation Sequencing (NGS) in order to compare them with international outbreak-associated Ab strains and to identify MLST (multi-locus sequence type) lineages, as well as to identify known resistance genes. Accordingly, NGS indicated higher diversity than rep-PCR, but also confirmed likely transmission events. The identified acquired carbapenem-resistant genes comprised blaOXA-23, blaOXA-72 and blaGES-12, as well as various other intrinsic and acquired resistance-associated genetic elements. All isolates clustered with the previously identified international clonal lineages IC1, IC2, IC6 and IC7, with corresponding Pasteur sequence types ST1, ST2, ST78 and ST25, respectively. In conclusion, the assessment confirmed a broad spectrum of resistance-associated genes in Ab isolated from war-injured patients from the Eastern Ukraine, and provided the first insights into locally abundant clonal lineages.

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Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan

Frontiers in Microbiology ◽

10.3389/fmicb.2021.628736 ◽

2021 ◽

Vol 12 ◽

Author(s):

Leena Al-Hassan ◽

Hana Elbadawi ◽

Einas Osman ◽

Sara Ali ◽

Kamal Elhag ◽

...

Keyword(s):

Antibiotic Resistance ◽

Molecular Epidemiology ◽

Acinetobacter Baumannii ◽

Core Genome ◽

Treatment Options ◽

Resistance Mechanisms ◽

Multiple Antibiotic Resistance ◽

Resistance Determinants ◽

Carbapenem Resistant ◽

Allelic Differences

Carbapenem resistant Acinetobacter baumannii (CRAb) is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients, due to limited alternative treatment options. Nine international clonal (IC) lineages have been identified in many countries worldwide, however, data still lacks from some parts of the world, particularly in Africa. We hereby present the molecular epidemiology of MDR A. baumannii from four hospitals in Khartoum, Sudan, collected from 2017 to 2018. Forty-two isolates were whole-genome sequenced, and subsequent molecular epidemiology was determined by core genome MLST (cgMLST), and their resistomes identified. All isolates had an array of diverse antibiotic resistance mechanisms conferring resistance to multiple classes of antibiotics. We found a predominance (88%) of IC2 (with the intrinsic OXA-66 and acquired OXA-23), and some with NDM-1. IC2 isolates were sub-divided into 4 STs separated by 5 to 431 allelic differences, and with evidence of seven transmission clusters. Isolates belonging to IC1, IC5, and IC9 were also identified. These data illustrate that MDR IC2 A. baumannii are widely distributed in Khartoum hospitals and are in possession of multiple antibiotic resistance determinants.

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Molecular dissection of Carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals using Whole Genome Sequencing

10.1101/2021.07.30.454432 ◽

2021 ◽

Author(s):

Steffimol Rose ◽

Varun Shamanna ◽

Anthony Underwood ◽

Geetha Nagaraj ◽

Akshatha Prasanna ◽

...

Keyword(s):

Molecular Epidemiology ◽

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Clonal Complex ◽

Carbapenem Resistance ◽

Evolutionary Divergence ◽

Whole Genome ◽

Northern India ◽

Carbapenem Resistant

Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) has acquired worldwide recognition as a serious nosocomial infection. It poses a concern to hospitalized patients because of the limited therapeutic options available. Thus, we investigated the molecular epidemiology and antibiotic resistance profiles of A. baumannii isolates in India. Materials and Methods: We characterized 306 retrospective A. baumannii clinical isolates collected from 18 centers across 10 states and 1 Union Territory of India between 2015 and 2019. Molecular epidemiology, and carbapenem resistance were studied by Whole Genome Sequencing. Results: A total of 105 different Sequence Types (STs) were identified including 48 reported STs and 57 Novel STs. 99 isolates were classified into Clonal Complex 451 (CC451) among which ST848 and ST1956 were the common STs. Carbapenemase resistance was confirmed in all the isolates with the presence of intrinsic bla OXA -51-like genes, and the acquired bla OXA-23 and bla NDM-1 genes. Conclusion: Most of the isolates were grouped under clonal complex 451. ST1053 caused an outbreak in Northern India during 2018 and 2019. Novel MLST alleles and STs were also detected, underlining an evolutionary divergence in India. The carbapenem-resistance was dominated by OXA-type carbapenemases and further surveillance of these carbapenem-resistant A. baumannii and antimicrobial stewardship should be strengthened.

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Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates from Northern Africa and the Middle East

Antibiotics ◽

10.3390/antibiotics10030291 ◽

2021 ◽

Vol 10 (3) ◽

pp. 291

Author(s):

Paul G. Higgins ◽

Ralf Matthias Hagen ◽

Bernd Kreikemeyer ◽

Philipp Warnke ◽

Andreas Podbielski ◽

...

Keyword(s):

Middle East ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Core Genome ◽

Carbapenem Resistance ◽

Resistance Mechanisms ◽

Northern Africa ◽

Carbapenem Resistant ◽

Next Generation Sequencing Ngs ◽

Injured Patients

At the Bundeswehr Hospitals of Hamburg and Westerstede, patients repatriated from subtropical war and crisis zones of Northern Africa and the Middle East were medically treated, including microbiological assessment. Within a six-year interval, 16 Acinetobacter spp. strains, including 14 Acinetobacter baumannii (Ab) isolates with resistance against carbapenems and origins in Afghanistan (n = 4), Iraq (n = 2), Libya (n = 2), and Syria (n = 8) were collected. While clonal relationships of Libyan and Syrian strains had been assessed by superficial next generation sequencing (NGS) and “DiversiLab” repetitive elements sequence-based (rep-)PCR so far, this study provides core genome-based sequence typing and thus more detailed epidemiological information. In detail, sequencing allowed a definitive species identification and comparison with international outbreak-associated Ab strains by core genome multi locus sequence typing (cgMLST) and the identification of MLST lineages, as well as the identification of known resistance genes. The sequence analysis allowed for the confirmation of outbreak-associated clonal clusters among the Syrian and Afghan Ab isolates, indicating likely transmission events. The identified acquired carbapenem resistance genes comprised blaOXA-23, blaOXA-58, blaNDM-1, and blaGES-11, next to other intrinsic and acquired, partly mobile resistance-associated genes. Eleven out of 14 Ab isolates clustered with the previously described international clonal lineages IC1 (4 Afghan strains), IC2 (6 Syrian strains), and IC7 (1 Syrian strain). Identified Pasteur sequence types of the 14 Ab strains comprised ST2 (Syrian), ST25 (Libyan), ST32 (Iraqi), ST81 (Afghan), ST85 (Libyan), and ST1112 (Syrian), respectively. In conclusion, the study revealed a broad spectrum of resistance genes in Ab isolated from war-injured patients from Northern Africa and the Middle East, thereby broadening the scarcely available data on locally abundant clonal lineages and resistance mechanisms.

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WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia

Antibiotics ◽

10.3390/antibiotics10050563 ◽

2021 ◽

Vol 10 (5) ◽

pp. 563

Author(s):

Gamal Wareth ◽

Jörg Linde ◽

Ngoc H. Nguyen ◽

Tuan N. M. Nguyen ◽

Lisa D. Sprague ◽

...

Keyword(s):

Southeast Asia ◽

Acinetobacter Baumannii ◽

Core Genome ◽

Action Plan ◽

Carbapenem Resistant ◽

Global Threat ◽

Next Generation Sequencing Ngs ◽

Sequence Types ◽

Generation Sequencing

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3”)-IIa, armA, aph(6)-Id and aph(3”) genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains. A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3”)-IIa, aph(3”)-Ib, aph(6)-Id, armA and aph(3’)-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.

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Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.633817 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xiufeng Zhang ◽

Fangping Li ◽

Furqan Awan ◽

Hongye Jiang ◽

Zhenling Zeng ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Insertion Sequence ◽

Core Genome ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Chi Square ◽

The Core ◽

Carbapenem Resistant ◽

Significant Difference ◽

Chi Square Test

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried blaOXA-23, blaOXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.

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Effect of carbapenem consumption patterns on the molecular epidemiology and carbapenem resistance of Acinetobacter baumannii

Journal of Medical Microbiology ◽

10.1099/jmm.0.082818-0 ◽

2014 ◽

Vol 63 (12) ◽

pp. 1654-1662 ◽

Cited By ~ 8

Author(s):

Julianna Mózes ◽

Fatemeh Ebrahimi ◽

Orsolya Gorácz ◽

Cecília Miszti ◽

Gábor Kardos

Keyword(s):

Molecular Epidemiology ◽

Acinetobacter Baumannii ◽

Carbapenem Resistance ◽

Antibiotic Consumption ◽

Positive Sample ◽

Carbapenem Resistant ◽

Defined Daily Doses ◽

Bed Days ◽

The University ◽

Multiple Clusters

This study investigated the molecular epidemiology of Acinetobacter baumannii in the University of Debrecen in relation to antibiotic consumption. Overall and ward-specific antibiotic consumption was measured by the number of defined daily doses (DDD) per 100 bed-days between 2002 and 2012. Consumption was analysed against the number of A. baumannii positive patients per 100 bed-days, number of isolates per positive sample, and proportion of carbapenem resistant A. baumannii, using time-series analysis. Altogether 160 A. baumannii isolates from different wards were collected and analysed. Carbapenemase genes blaOXA-23-like , blaOXA-24-like , blaOXA-48-like , blaOXA-51-like , blaOXA-58-like and integrons were sought by PCR. Relatedness of isolates was assessed by PFGE. Prevalence and carbapenem resistance of A. baumannii were statistically associated with carbapenem consumption. Prevalence data followed carbapenem usage with three quarterly lags (r = 0.51–0.53, P<0.001), and meropenem and ertapenem, but not imipenem usage, affected prevalence. Colistin usage, in turn, lagged behind prevalence with one lag (r = 0.68–0.70, P<0.001). Six clusters were identified; the neurology ward with the lowest carbapenem consumption was associated with the carbapenem-susceptible cluster, as well as with the carbapenem-susceptible isolates in the cluster with variable susceptibility. Wards with high carbapenem usage almost exclusively harboured isolates from carbapenem-resistant clusters. All clusters were dominated by isolates of one or two wards, but most wards were represented in multiple clusters. Increases in prevalence and carbapenem resistance of A. baumannii were associated with usage of meropenem and ertapenem but not of imipenem, which led to the spread of multiple clones in the University.

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