Persistence of Multiple Antibiotic Resistant Strains ofAcinetobacter baumanniiCarrying Class 1 Integron in a Hospital Setting

Background and Aim: Salmonella is one of the most common foodborne pathogens, the emergence of antibiotic-resistant strains of which is increasing. The aim of this study was to phenotypically and genotypically characterize the fluoroquinolone resistance of Salmonella isolates from broiler and humans in two regions of Colombia. Materials and Methods: Salmonella strains (n=49) were evaluated. The phenotype of antibiotic resistance was assessed by an automated method and agar diffusion method, as well as the presence of the quinolone resistance genes qnrA, qnrB, qnrC, qnrD, qnrS, and aac(6')-Ib as determined by polymerase chain reaction. Results: Strains were resistant to ciprofloxacin (75%), levofloxacin (57.1%), and enrofloxacin (38.8%). Molecular identification showed that 24 out of 49 strains possessed the qnrB gene (48.9%), while only one isolate from the Santander region possessed the aac(6')-Ib gene. Regarding Class 1 integron, it was present in 11 out of the 49 strains (22.44%). Conclusion: This study reports the presence of the gene qnrB as well the presence of Class 1 integrons in broiler Salmonella isolates, which may contribute to the resistance to fluoroquinolones.

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Antibiotic resistance profile of Salmonella enterica isolated from exotic and indigenous leafy green vegetables in Accra, Ghana

Journal of Food Protection ◽

10.4315/jfp-20-442 ◽

2021 ◽

Author(s):

Jinru Chen ◽

Joycelyn Quansah

Keyword(s):

Antibiotic Resistance ◽

Salmonella Enterica ◽

Gene Cassette ◽

Nucleotide Sequencing ◽

Dilution Method ◽

Class 1 Integron ◽

Antibiotic Resistant ◽

Resistance Profile ◽

Antibiotic Resistance Profile ◽

Class 1

Fresh produce-borne enteric bacterial pathogens with resistance to antibiotics have posed serious challenges to food safety and public health worldwide. This study examined the antibiotic resistance profile of Salmonella enterica (n=33), previously isolated from exotic and indigenous leafy green vegetable samples (n=328) collected from 50 vegetable farms in 12 farming areas and 37 vegetable sellers in 4 market centers in Accra, Ghana during the period of March 2016 to March 2017, and determined the distribution of integrons among antibiotic-resistant isolates. The susceptibility of the Salmonella isolates to 12 antibiotics was assayed using the standard disc diffusion assay. The minimum inhibitory concentrations (MICs) of the five most resisted antibiotics were determined using the twofold macro dilution method. PCR assay was used to detect the presence of integrons in Salmonella cells, and PCR product with amplified integron gene cassette was purified and sequenced using the Sanger sequencing technology. The Salmonella isolates used in the study resisted at least one tested antibiotic, and multi-drug resistant (MDR) isolates were 30.3% (10/33). Most isolates (81.8%) were resistant to sulfisoxazole. The MICs of tetracycline, cefoxitin, streptomycin, ampicillin, and sulfisoxazole were 16, 32, 64, 64, and > 1,024 µg/ml, respectively. A total of five different patterns of MDR were observed among the Salmonella isolates, and the common MDR patterns were AAuFox (30.3%) and AAuFoxSSu (18.1%). One out of the 33 (3.0%) Salmonella isolates tested positive for class 1 integron with a gene cassette of about 800 bp. Nucleotide sequencing revealed the class 1 integron carried a single gene dfrA7 . Future studies are needed to confirm whether the consumption of contaminated leafy green vegetables is a route of acquiring antibiotic-resistant Salmonella by consumers in Accra, Ghana.

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SGI1-K, a Variant of the SGI1 Genomic Island Carrying a Mercury Resistance Region, in Salmonella enterica Serovar Kentucky

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01229-06 ◽

2006 ◽

Vol 51 (1) ◽

pp. 317-323 ◽

Cited By ~ 43

Author(s):

Renee S. Levings ◽

Sally R. Partridge ◽

Steven P. Djordjevic ◽

Ruth M. Hall

Keyword(s):

Salmonella Enterica ◽

Genomic Island ◽

Mercury Resistance ◽

Variant Form ◽

Short Segment ◽

Class 1 Integron ◽

Antibiotic Resistant ◽

Right Hand ◽

Class 1 ◽

The Right

ABSTRACT A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3′-conserved segment (3′-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3′-CS and IS6100 in In4 family integrons, has been removed by an IS6100-mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn501 and Tn21. This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.

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Multiniche Screening Reveals the Clinically Relevant Metallo-β-Lactamase VIM-2 in Pseudomonas aeruginosa Far from the Hospital Setting: an Ongoing Dispersion Process?

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3743-3745.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3743-3745 ◽

Cited By ~ 30

Author(s):

Sandra Quinteira ◽

Luï¿½sa Peixe

Keyword(s):

Pseudomonas Aeruginosa ◽

Hospital Setting ◽

Aquatic Habitats ◽

Class 1 Integron ◽

Dispersion Process ◽

Class 1 ◽

Screening Study

ABSTRACT A screening study of the presence of metallo-β-lactamases (IMP and VIM types and SPM-1) in isolates from different nonhospital sources was conducted, and it revealed the presence of bla VIM-2, associated with the In58 class 1 integron, in two unrelated Pseudomonas aeruginosa strains from aquatic habitats. The results suggest that the hospital setting was the possible origin of these bla VIM-2-carrying strains.

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A Novel, Integron-Regulated, Class C β-Lactamase

Antibiotics ◽

10.3390/antibiotics9030123 ◽

2020 ◽

Vol 9 (3) ◽

pp. 123

Author(s):

Maria-Elisabeth Böhm ◽

Mohammad Razavi ◽

Carl-Fredrik Flach ◽

D. G. Joakim Larsson

Keyword(s):

Bacterial Infections ◽

Gene Cassette ◽

Fourth Generation ◽

Resistance Pattern ◽

Asian Countries ◽

Class 1 Integron ◽

Class 1 ◽

Resistant Strains ◽

Class C ◽

Mobile Context

AmpC-type β-lactamases severely impair treatment of many bacterial infections, due to their broad spectrum (they hydrolyze virtually all β-lactams, except fourth-generation cephalosporins and carbapenems) and the increasing incidence of plasmid-mediated versions. The original chromosomal AmpCs are often tightly regulated, and their expression is induced in response to exposure to β-lactams. Regulation of mobile ampC expression is in many cases less controlled, giving rise to constitutively resistant strains with increased potential for development or acquisition of additional resistances. We present here the identification of two integron-encoded ampC genes, blaIDC-1 and blaIDC-2 (integron-derived cephalosporinase), with less than 85% amino acid sequence identity to any previously annotated AmpC. While their resistance pattern identifies them as class C β-lactamases, their low isoelectric point (pI) values make differentiation from other β-lactamases by isoelectric focusing impossible. To the best of our knowledge, this is the first evidence of an ampC gene cassette within a class 1 integron, providing a mobile context with profound potential for transfer and spread into clinics. It also allows bacteria to adapt expression levels, and thus reduce fitness costs, e.g., by cassette-reshuffling. Analyses of public metagenomes, including sewage metagenomes, show that the discovered ampCs are primarily found in Asian countries.

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Two New SGI1-LK Variants Found in Proteus mirabilis and Evolution of the SGI1-HKL Group of Salmonella Genomic Islands

mSphere ◽

10.1128/msphere.00875-19 ◽

2020 ◽

Vol 5 (2) ◽

Cited By ~ 2

Author(s):

Claire de Curraize ◽

Eliane Siebor ◽

Véronique Varin ◽

Catherine Neuwirth ◽

Ruth M. Hall

Keyword(s):

Homologous Recombination ◽

Proteus Mirabilis ◽

Salmonella Enterica ◽

Genomic Islands ◽

Class 1 Integron ◽

Antibiotic Resistant ◽

Content Type ◽

Novel Variants ◽

Class 1 ◽

Complex Forms

ABSTRACT Integrative mobilizable elements belonging to the SGI1-H, -K, and -L Salmonella genomic island 1 (SGI1) variant groups are distinguished by the presence of an alteration in the backbone (IS1359 replaces 2.8 kb of the backbone extending from within traN [S005] to within S009). Members of this SGI1-HKL group have been found in Salmonella enterica serovars and in Proteus mirabilis. Two novel variants from this group, designated SGI1-LK1 and SGI1-LK2, were found in the draft genomes of antibiotic-resistant P. mirabilis isolates from two French hospitals. Both variants can be derived from SGI1-PmGUE, a configuration found previously in another P. mirabilis isolate from France. SGI1-LK1 could arise via an IS26-mediated inversion in the complex class 1 integron that duplicated the IS26 element and the target site in IS6100. SGI1-LK1 also has a larger 8.59-kb backbone deletion extending from traN to within S013 and removing traG and traH. However, SGI1-LK1 was mobilized by an IncC plasmid. SGI1-LK2 can be derived from a hypothetical progenitor, SGI1-LK0, that is related to SGI1-PmGUE but lacks the aphA1 gene and one copy of IS26. The integron of SGI1-LK2 could arise via deletion of DNA adjacent to an IS26 and a deletion occurring via homologous recombination between duplicated copies of part of the integron 3′-conserved segment. SGI1-K can also be derived from SGI1-LK0. This would involve an IS26-mediated deletion and an inversion via homologous recombination of a segment between inversely oriented IS26s. Similar events can explain the configuration of the integrons in other SGI1-LK variants. IMPORTANCE Members of the SGI1-HKL subgroup of SGI1-type integrative mobilizable elements have a characteristic alteration in their backbone. They are widely distributed among multiply antibiotic-resistant Salmonella enterica serovars and Proteus mirabilis isolates. The SGI1-K type, found in the globally disseminated multiply antibiotic-resistant Salmonella enterica serovar Kentucky clone ST198 (sequence type 198), and various configurations in the original SGI1-LK group, found in other multiresistant S. enterica serovars and Proteus mirabilis isolates, have complex and highly plastic resistance regions due to the presence of IS26. However, how these complex forms arose and the relationships between them had not been analyzed. Here, a hypothetical progenitor, SGI1-LK0, that can be formed from the simpler SGI1-H is proposed, and the pathways to the formation of new variants, SGI1-LK1 and SGI1-LK2, found in P. mirabilis and other reported configurations via homologous recombination and IS26-mediated events are proposed. This led to a better understanding of the evolution of the SGI1-HKL group.

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Characterization of antibiotic resistance genes linked to class 1 and 2 integrons in strains of Salmonella spp. isolated from swine

Canadian Journal of Microbiology ◽

10.1139/w08-045 ◽

2008 ◽

Vol 54 (7) ◽

pp. 569-576 ◽

Cited By ~ 17

Author(s):

Betty San Martín ◽

Lisette Lapierre ◽

Javiera Cornejo ◽

Sergio Bucarey

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Agents ◽

Antibiotic Resistance Genes ◽

Dilution Method ◽

Salmonella Spp ◽

Class 1 Integron ◽

Resistance Determinants ◽

Class 1 ◽

Resistant Strains

The aim of this study was to characterize the antibiotic resistance profiles, the integron-associated resistance determinants, and the potential ability of transferring these determinants by conjugation in Salmonella enterica isolated from swine. Fifty-four strains of Salmonella spp. were isolated from healthy swine. The percentages of resistance, determined by the plate dilution method were as follows: oxytetracycline (41%), streptomycin (39%), sulphamethoxazol+trimethoprim (19%), enrofloxacin–ciprofloxacin (13%), and amoxicillin (0%). The most important resistance serovars were Salmonella Branderburg, Salmonella Derby, Salmonella Typhimurium, and Salmonella Heidelberg. The oxytetracycline-resistant strains amplified the genes tetA (36%), tetB (64%); and the strains resistant to streptomycin and trimethoprim amplified the genes aadA1 (100%) and dfrA1 (100%), respectively. None of the fluoroquinolone-resistant strains amplified the gene qnr. Ten strains amplified the class 1 integron harboring the cassette aadA1. Six strains amplified the class 2 integron harboring the cassettes dfrA1, sat1, and aadA1. The conjugation assays showed that 2 strains transferred the tetA and aadA1 genes and the class 1 integron to a recipient strain. Taken together, the results obtained in this study show a high percentage of resistance in and the presence of integrons in strains of S. enterica isolated from swine. This information should support the implementation of regulations for the prudent use of antimicrobial agents in food-producing animals.

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The household resistome – frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment

10.1101/2020.06.04.135590 ◽

2020 ◽

Author(s):

Laura Schages ◽

Ralf Lucassen ◽

Florian Wichern ◽

Rainer Kalscheuer ◽

Dirk Bockmühl

Keyword(s):

Antibiotic Resistance ◽

Resistant Bacteria ◽

Beta Lactamase ◽

Class 1 Integron ◽

Domestic Environment ◽

Private Households ◽

Washing Machines ◽

Class 1 ◽

Potential Reservoir ◽

Resistant Strains

AbstractThe widespread of antibiotic resistance (ABR) among bacteria has become a global health concern for humans, animals and the environment. In this respect, beta-lactams and colistin are of particular interest due to the emergence of multidrug-resistant gram-negative bacteria. Households provide a habitat for bacteria originating from humans, animals, foods, contaminated clothes or other sources in which detergents and biocides are frequently used. Thus, bacteria carrying antibiotic resistance genes (ARGs) might be introduced into private households and may consequently be also released from households to the environment via domestic wastewater. Since data on ABR in the domestic environment is limited, this study aimed to determine the abundance and correlation of beta-lactamase, mobile colistin resistance and class 1 integron genes and to characterize phenotypic resistant strains in private households in Germany. Additionally, the persistence of ABR bacteria to laundering and automated dishwashing was assessed. Shower drains, washing machines and dishwashers were sampled and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of ARGs in shower drains compared to washing machines and dishwashers. Several beta-lactamase genes co-occurred and resistance of bacterial isolates correlated positively with genotypic resistance. Laundering and automated dishwashing reduced ABR bacteria significantly and the efficacy increased with increasing duration and temperature. Overall, the domestic environment seems to represent a potential reservoir of beta-lactamase genes and beta-lactam resistant bacteria with shower drains as the dominant source of ABR.ImportanceThe abundance of ABR bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods or wastewater treatment plants. Despite of their connection to these environments, private households seem to be neglected. Therefore, the present study investigated shower drains, washing machines and dishwashers as possible sites of ARGs and ABR bacteria. The analysis of the domestic environment as a potential reservoir of resistant bacteria is crucial to determine whether households contribute to the spread of ABR or are a habitat where resistant bacteria from the environment, humans, food or water accumulate.

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Megaplasmids on the Rise: Combining Sequencing Approaches to Fully Resolve a Carbapenemase-Encoding Plasmid in a Proposed NovelPseudomonasSpecies

10.1101/601898 ◽

2019 ◽

Author(s):

João Botelho ◽

Cédric Lood ◽

Sally R. Partridge ◽

Vera van Noort ◽

Rob Lavigne ◽

...

Keyword(s):

Hospital Setting ◽

Antibiotic Resistance Genes ◽

Heavy Metal Resistance ◽

Multidrug Resistant ◽

Metal Resistance ◽

Resistant Bacteria ◽

Class 1 Integron ◽

Routine Surveillance ◽

Class 1 ◽

Selective Forces

AbstractHorizontal transfer of plasmids plays a pivotal role in the dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Sequencing of plasmids is thus paramount for the success of accurate epidemiological tracking strategies in the hospital setting and routine surveillance. Here, we combine Nanopore and Illumina sequencing to fully assemble a carbapenemase-encoding megaplasmid carried by a clinical isolate belonging to a putative novelPseudomonasspecies. FFUP_PS_41 has a multidrug resistance phenotype and was initially identified asPseudomonas putida, but an average nucleotide identity below the cut-off for species delineation suggests a new species related to theP. putidaphylogenetic group. FFUP_PS_41 harbors a 498,516-bp untypable megaplasmid (pJBCL41) with low similarity compared with publicly available plasmids. pJBCL41 contains a full set of genes for self-transmission and genes predicted to be responsible for plasmid replication, partitioning, maintenance and heavy metal resistance. pJBCL41 carries a class 1 integron with the |aacA7|blaVIM-2|aacA4| cassette array (In103) located within a defective Tn402-like transposon that forms part of a 50,273-bp mosaic region bound by 38-bp inverted repeats typical of the Tn3family and flanked by 5-bp direct repeats. This region is composed of different elements, including additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach resulted in contiguous assemblies and allowed us to fully resolve a carbapenemase-encoding megaplasmid fromPseudomonasspp. The identification of novel megaplasmids will shed a new light on the evolutionary effects of gene transfer and the selective forces driving AR.

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AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa266 ◽

2020 ◽

Vol 75 (10) ◽

pp. 2760-2768 ◽

Cited By ~ 1

Author(s):

Agnes P Chan ◽

Yongwook Choi ◽

Thomas H Clarke ◽

Lauren M Brinkac ◽

Richard C White ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Insertion Site ◽

Clinical Isolates ◽

Genomic Context ◽

Class 1 Integron ◽

Antibiotic Resistant ◽

Short Reads ◽

Class 1 ◽

Assembly Technology ◽

Resistance Island

Abstract Objectives To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. Methods Using a combination of long and short reads generated from the Oxford Nanopore and Illumina platforms, contiguous chromosomes and plasmid sequences were determined. BLAST-based analysis was used to identify the RI insertion target. Results Genomes of four multiply antibiotic-resistant A. baumannii clinical strains, from a US hospital system, belonging to prevalent MLST ST2 (Pasteur scheme) and ST281 (Oxford scheme) clade F isolates were sequenced to completion. A class 1 integron carrying aadB (tobramycin resistance) and aadA2 (streptomycin/spectinomycin resistance) was identified. The class 1 integron was 6.8 kb, bounded by IS26 at both ends, and embedded in a new target location between an α/β-hydrolase and a reductase. Due to its novel insertion site and unique RI composition, we suggest naming this novel RI AbGRI4. Molecular analysis of global A. baumannii isolates identified multiple AbGRI4 RI variants in non-ST2 clonal lineages, including variations in the resistance gene cassettes, integron backbone and insertion breakpoints at the hydrolase gene. Conclusions A novel RI insertion target harbouring a class 1 integron was identified in a subgroup of ST2/ST281 clinical isolates. Variants of the RI suggested evolution and horizontal transfer of the RI across clonal lineages. Long- and short-read hybrid assembly technology completely resolved the genomic context of IS-bounded RIs, which was not possible using short reads alone.

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