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

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00277-21 ◽

2021 ◽

Author(s):

Antoine G. Abou Fayad ◽

Louis-Patrick Haraoui ◽

Ahmad Sleiman ◽

Mohamad Jaafar ◽

Abdulaziz Zorgani ◽

...

Keyword(s):

Molecular Epidemiology ◽

Acinetobacter Baumannii ◽

Doubling Time ◽

Core Genome ◽

Carbapenem Resistance ◽

Relative Fitness ◽

Fitness Advantage ◽

Carbapenem Resistant ◽

Sequence Types ◽

Hospital Transmission

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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679. Predominance of Acinetobacter baumannii Sequence Type 2 (ST2) among Clinical Isolates from Two Detroit Hospitals using Whole Genome Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.871 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S392-S393

Author(s):

Piyali Chatterjee ◽

Chetan Jinadatha ◽

Keith S Kaye ◽

Hosoon Choi ◽

Yonhui Allton ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Minimum Spanning Tree ◽

Veterans Affairs ◽

Sequence Type ◽

Whole Genome ◽

Healthcare Associated Infections ◽

Department Of Veterans Affairs ◽

Healthcare Associated ◽

Sequence Types ◽

Research Grant

Abstract Background Healthcare-associated infections (HAIs) caused by Acinetobacter baumannii, an opportunistic gram-negative pathogen, often contribute to morbidity and mortality among hospitalized patients. To determine molecular epidemiology of circulating hospital Acinetobacter strains in Detroit area in a non-outbreak situation, we performed whole genome sequencing (WGS) and whole genome multilocus sequence typing (wgMLST) analysis to characterize genomic diversity. Methods We performed WGS on patient isolates from two disparate, geographically distinct tertiary care Detroit hospitals admitted to 16 intensive care units (ICU) and non-ICU wards between 2017-2019. The samples were obtained 48 hours following admission and WGS was performed using the Illumina NextSeq instrument. The contigs were de novo assembled using SPAdes and WgMLST analysis was performed using BioNumerics software v7.6. Minimum spanning tree (MST) was constructed to demonstrate the clusters in each hospital and their wards. Results WgMLST analysis was performed on a total of 62 Acinetobacter baumannii patient isolates, 33 of which were from hospital # 1 (H1) and 29 were from hospital # 2 (H2). ST2 (52%) was the predominant sequence type for both hospitals. In addition to ST2, ST93 (8%) and ST406 (8%) clusters were also found in H1. Most of the isolates were predominantly clustered in the intensive care unit (ICU) setting. Several identical sequence types of ST93 (2 identical in H1), ST36 (2 identical in H1) and ST2 (5 identical for H1 and 2 identical for H2) were also observed from different patients in both hospitals. Unlike H1, H2 only has ST2 as a predominant cluster. Other sporadic sequence types such as ST119, ST36, ST49, ST212, ST667 for H1 and ST395, ST214, ST427 and ST268 for H2 were also observed. Figure 1. MInimum Spanning Tree of Acinetobacter strains in hospitals (H1 and H2) and different wards (U1-U12). For identical strains circles are marked with dividing lines. Different sequence types (STs) are marked om the side bar. Conclusion Our data suggests that ST2 is the predominant sequence type circulating in both the geographically distinct hospitals and is endemic to the ICU. There was in hospital spread of this distinct Acinetobacter sequence type from one patient to the other, raising concerns about infection control practices and the role of environment in the spread of these infections. Early detection of these endemic strains within the hospital may be critical in preventing healthcare-associated infections in the future. Disclosures Chetan Jinadatha, MD, MPH, AHRQ (Research Grant or Support)Department of Veterans Affairs (Other Financial or Material Support, Owner: Department of Veterans Affairs. Licensed to: Xenex Disinfection System, San Antonio, TX)Inventor (Other Financial or Material Support, Methods for organizing the disinfection of one or more items contaminated with biological agents)NiH/NINR (Research Grant or Support)NSF (Research Grant or Support)Xenex Healthcare Services (Research Grant or Support) Mark Stibich, PhD MHS, Xenex Disinfection Services, Inc (Board Member, Employee)

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First Description of Two Sequence Type 2 Acinetobacter baumannii Isolates Carrying OXA-23 Carbapenemase in Pagellus acarne Fished from the Mediterranean Sea near Bejaia, Algeria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02384-15 ◽

2016 ◽

Vol 60 (4) ◽

pp. 2513-2515 ◽

Cited By ~ 16

Author(s):

Soumia Brahmi ◽

Abdelaziz Touati ◽

Axelle Cadière ◽

Nassima Djahmi ◽

Alix Pantel ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Mediterranean Sea ◽

Sequence Type ◽

Content Type ◽

Carbapenem Resistant ◽

Selective Agar ◽

Agar Media ◽

The Mediterranean ◽

First Time

ABSTRACTTo determine the occurrence of carbapenem-resistantAcinetobacter baumanniiin fish fished from the Mediterranean Sea near the Bejaia coast (Algeria), we studied 300 gills and gut samples that had been randomly and prospectively collected during 1 year. After screening on selective agar media, using PCR arrays and whole-genome sequencing, we identified for the first time two OXA-23-producingA. baumanniistrains belonging to the widespread sequence type 2 (ST2)/international clone II and harboring aminoglycoside-modifying enzymes [aac(6′)-Ib andaac(3′)-I genes].

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Comparative Analysis of Carbapenem-Resistant Acinetobacter baumannii Sequence Types in Southern Brazil: From the First Outbreak (2007–2008) to the Endemic Period (2013–2014)

Microbial Drug Resistance ◽

10.1089/mdr.2018.0262 ◽

2019 ◽

Vol 25 (4) ◽

pp. 538-542 ◽

Cited By ~ 5

Author(s):

Mariana Pagano ◽

Luciana S. Nunes ◽

Marina Niada ◽

Afonso Luís Barth ◽

Andreza F. Martins

Keyword(s):

Comparative Analysis ◽

Acinetobacter Baumannii ◽

Southern Brazil ◽

Carbapenem Resistant ◽

Sequence Types

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The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03954-14 ◽

2014 ◽

Vol 59 (1) ◽

pp. 427-436 ◽

Cited By ~ 135

Author(s):

Veronica N. Kos ◽

Maxime Déraspe ◽

Robert E. McLaughlin ◽

James D. Whiteaker ◽

Paul H. Roy ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Genetic Determinants ◽

Content Type ◽

Susceptibility Data ◽

Next Generation Sequencing Ngs ◽

Sequence Types ◽

Generation Sequencing ◽

Phenotypic Susceptibility

ABSTRACTMany clinical isolates ofPseudomonas aeruginosacause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates ofP. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants withinP. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment ofP. aeruginosainfections.

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