Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities

Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse of antibiotics. Nowadays, the prevalence of these kinds of emerging contaminants in shrimp aquaculture environments is still unclear. In this study, high-throughput sequencing techniques were used to analyze the distribution of ARGs and mobile genetic elements (MGEs), bacterial communities, and their correlations in water and sediment samples in two types of typical shrimp (Procambarus clarkii and Macrobrachium rosenbergii) freshwater aquaculture environments. A total of 318 ARG subtypes within 19 ARG types were detected in all the samples. The biodiversity and relative abundance of ARGs in sediment samples showed much higher levels compared to water samples from all ponds in the study area. Bacitracin (17.44–82.82%) and multidrug (8.57–49.70%) were dominant ARG types in P. clarkii ponds, while sulfonamide (26.33–39.59%) and bacitracin (12.75–37.11%) were dominant ARG types in M. rosenbergii ponds. Network analysis underlined the complex co-occurrence patterns between bacterial communities and ARGs. Proteobacteria, Cyanobacteria, and Actinobacteria exhibited a high abundance in all samples, in which C39 (OTU25355) and Hydrogenophaga (OTU162961) played important roles in the dissemination of and variation in ARGs based on their strong connections between ARGs and bacterial communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) and Microbacteriaceae (OTU16033)), which were potential hosts for various ARGs, may accelerate the propagation of ARGs and be harmful to human health via horizontal gene transfer mediated by MGEs. Variation partitioning analysis further confirmed that MGEs were the most crucial contributor (74.76%) driving the resistome alteration. This study may help us to understand the non-ignorable correlations among ARGs, bacterial diversity, and MGEs in the shrimp freshwater aquaculture environments.

Download Full-text

Mobile Genetic Elements Related to the Diffusion of Plasmid-Mediated AmpC β-Lactamases or Carbapenemases from Enterobacteriaceae: Findings from a Multicenter Study in Spain

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00562-15 ◽

2015 ◽

Vol 59 (9) ◽

pp. 5260-5266 ◽

Cited By ~ 13

Author(s):

L. Zamorano ◽

E. Miró ◽

C. Juan ◽

L. Gómez ◽

G. Bou ◽

...

Keyword(s):

Southern Hybridization ◽

Mobile Genetic Elements ◽

Pulsed Field Gel Electrophoresis ◽

Content Type ◽

Genetic Elements ◽

Chromosomal Origin ◽

Class 1 ◽

Rapid Dissemination ◽

Large Plasmids ◽

Genetic Context

ABSTRACTWe examined the genetic context of 74 acquiredampCgenes and 17 carbapenemase genes from 85 of 640Enterobacteriaceaeisolates collected in 2009. Using S1 pulsed-field gel electrophoresis and Southern hybridization, 37 of 74blaAmpCgenes were located on large plasmids of different sizes belonging to six incompatibility groups. We used sequencing and PCR mapping to investigate the regions flanking the acquiredampCgenes. TheblaCMY-2-like genes were associated with ISEcp1; the surroundingblaDHAgenes were similar toKlebsiella pneumoniaeplasmid pTN60013 associated with IS26and thepspandsapoperons; and theblaACC-1genes were associated with IS26elements inserted into ISEcp1. All of the carbapenemase genes (blaVIM-1,blaIMP-22, andblaIMP-28) were located in class 1 integrons. Therefore, although plasmids are the main cause of the rapid dissemination ofampCgenes amongEnterobacteriaceae, we need to be aware that other mobile genetic elements, such as insertion sequences, transposons, or integrons, can be involved in the mobilization of these genes of chromosomal origin. Additionally, three new integrons (In846 to In848) are described in this study.

Download Full-text

Black Queen Evolution and Trophic Interactions Determine Plasmid Survival after the Disruption of the Conjugation Network

mSystems ◽

10.1128/msystems.00104-18 ◽

2018 ◽

Vol 3 (5) ◽

Cited By ~ 6

Author(s):

Johannes Cairns ◽

Katariina Koskinen ◽

Reetta Penttinen ◽

Tommi Patinen ◽

Anna Hartikainen ◽

...

Keyword(s):

Antibiotic Resistance ◽

Bacterial Communities ◽

Resistance Mechanism ◽

Real Life ◽

Ecological Factors ◽

Mobile Genetic Elements ◽

Resistance Mechanisms ◽

Antibiotics Resistance ◽

Bacterial Populations ◽

Genetic Elements

ABSTRACTMobile genetic elements such as conjugative plasmids are responsible for antibiotic resistance phenotypes in many bacterial pathogens. The ability to conjugate, the presence of antibiotics, and ecological interactions all have a notable role in the persistence of plasmids in bacterial populations. Here, we set out to investigate the contribution of these factors when the conjugation network was disturbed by a plasmid-dependent bacteriophage. Phage alone effectively caused the population to lose plasmids, thus rendering them susceptible to antibiotics. Leakiness of the antibiotic resistance mechanism allowing Black Queen evolution (i.e. a “race to the bottom”) was a more significant factor than the antibiotic concentration (lethal vs sublethal) in determining plasmid prevalence. Interestingly, plasmid loss was also prevented by protozoan predation. These results show that outcomes of attempts to resensitize bacterial communities by disrupting the conjugation network are highly dependent on ecological factors and resistance mechanisms.IMPORTANCEBacterial antibiotic resistance is often a part of mobile genetic elements that move from one bacterium to another. By interfering with the horizontal movement and the maintenance of these elements, it is possible to remove the resistance from the population. Here, we show that a so-called plasmid-dependent bacteriophage causes the initially resistant bacterial population to become susceptible to antibiotics. However, this effect is efficiently countered when the system also contains a predator that feeds on bacteria. Moreover, when the environment contains antibiotics, the survival of resistance is dependent on the resistance mechanism. When bacteria can help their contemporaries to degrade antibiotics, resistance is maintained by only a fraction of the community. On the other hand, when bacteria cannot help others, then all bacteria remain resistant. The concentration of the antibiotic played a less notable role than the antibiotic used. This report shows that the survival of antibiotic resistance in bacterial communities represents a complex process where many factors present in real-life systems define whether or not resistance is actually lost.

Download Full-text

Characterization of a Novel Plasmid-Mediated Cephalosporinase (CMY-9) and Its Genetic Environment in an Escherichia coli Clinical Isolate

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.46.8.2427-2434.2002 ◽

2002 ◽

Vol 46 (8) ◽

pp. 2427-2434 ◽

Cited By ~ 41

Author(s):

Yohei Doi ◽

Naohiro Shibata ◽

Keigo Shibayama ◽

Kazunari Kamachi ◽

Hiroshi Kurokawa ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequence ◽

Gene Cassette ◽

Single Amino Acid ◽

Common Region ◽

Class 1 Integron ◽

Class 1 ◽

The Common ◽

High Level

ABSTRACT An Escherichia coli strain, HKYM68, which showed resistance to broad-spectrum cephalosporins was isolated from a sputum specimen in Japan. The high-level resistance of the strain to ceftazidime, cefpirome, and moxalactam was carried by a self-transferable plasmid. The β-lactamase gene responsible for the resistance was cloned and sequenced. The deduced amino acid sequence of this gene product, CMY-9, had a single amino acid substitution (E85D), the residue reported to be part of the recognition site for the R1 side chain of β-lactams, compared with the amino acid sequence of CMY-8 and also had 78% identity with the amino acid sequence of CepH, a chromosomal cephalosporinase of Aeromonas hydrophila. A sul1-type class 1 integron containing an aacA1-orfG gene cassette was identified upstream of bla CMY-9 and ended with a truncated 3′ conserved segment. The following 2.1 kb was almost identical to the common region of integrons In6 and In7 and the integron of pSAL-1, except that orf513 encoding a putative transposase was identified instead of orf341 due to addition of a single nucleotide. bla CMY-9 was closely located downstream of the end of the common region. These observations are indicative of the exogenous derivation of bla CMY-9 from some environmental microorganisms such as aeromonads.

Download Full-text

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.

Download Full-text

A Multispecies Cluster of VIM-1 Carbapenemase-Producing Enterobacterales Linked by a Novel, Highly Conjugative, and Broad-Host-Range IncA Plasmid Forebodes the Reemergence of VIM-1

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02435-19 ◽

2020 ◽

Vol 64 (4) ◽

Cited By ~ 2

Author(s):

Gabriele Arcari ◽

Federica Maria Di Lella ◽

Giulia Bibbolino ◽

Fabio Mengoni ◽

Marzia Beccaccioli ◽

...

Keyword(s):

Host Range ◽

Bacterial Species ◽

Klebsiella Oxytoca ◽

Gene Cassette ◽

University Hospital ◽

Broad Host Range ◽

Class 1 Integron ◽

Content Type ◽

Carbapenem Resistant ◽

Class 1

ABSTRACT In this study, we investigated VIM-1-producing Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Citrobacter freundii, and Enterobacter cloacae strains, isolated in 2019 during a period of active surveillance of carbapenem-resistant Enterobacterales in a large university hospital in Italy. VIM-1-producing strains colonized the gut of patients, with up to three different VIM-1-positive bacterial species isolated from a single rectal swab, but also caused bloodstream infection in one colonized patient. In the multispecies cluster, blaVIM-1 was identified in a 5-gene cassette class 1 integron, associated with several genetic determinants, including the blaSHV-12, qnrS1, and mph(A) genes, located on a highly conjugative and broad-host-range IncA plasmid. The characteristics and origin of this IncA plasmid were studied.

Download Full-text

First Detection of a Carbapenem-Hydrolyzing Metalloenzyme in Two Enterobacteriaceae Isolates in Spain

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.8.3492-3494.2005 ◽

2005 ◽

Vol 49 (8) ◽

pp. 3492-3494 ◽

Cited By ~ 38

Author(s):

M. Teresa Tórtola ◽

Susana Lavilla ◽

Elisenda Miró ◽

Juan José González ◽

Nieves Larrosa ◽

...

Keyword(s):

Escherichia Coli ◽

Klebsiella Pneumoniae ◽

Gene Cassette ◽

Class 1 Integron ◽

Class 1 ◽

First Time

ABSTRACT Two strains of Enterobacteriaceae, Escherichia coli and Klebsiella pneumoniae, producing VIM-1 were isolated for the first time in Spain. In both strains, bla VIM-1 was found to be carried on a gene cassette inserted into a class 1 integron. The bla VIM-1-containing integron was located on a transferable plasmid.

Download Full-text

A Predominant Multidrug-Resistant Salmonella enterica Serovar Saintpaul Clonal Line in German Turkey and Related Food Products

Applied and Environmental Microbiology ◽

10.1128/aem.02744-09 ◽

2010 ◽

Vol 76 (11) ◽

pp. 3657-3667 ◽

Cited By ~ 16

Author(s):

Janine Beutlich ◽

Irene RodrÃ¯Â¿Â½guez ◽

Andreas Schroeter ◽

Annemarie KÃ¯Â¿Â½sbohrer ◽

Reiner Helmuth ◽

...

Keyword(s):

Salmonella Enterica ◽

Food Products ◽

Gene Cassette ◽

Multidrug Resistant ◽

Resistance Pattern ◽

Clonal Line ◽

Class 1 Integron ◽

Pathogenic Potential ◽

Class 1 ◽

Plasmid Profiling

ABSTRACT Recently, Salmonella enterica subsp. enterica serovar Saintpaul has increasingly been observed in several countries, including Germany. However, the pathogenic potential and epidemiology of this serovar are not very well known. This study describes biological attributes of S. Saintpaul isolates obtained from turkeys in Germany based on characterization of their pheno- and genotypic properties. Fifty-five S. Saintpaul isolates from German turkeys and turkey-derived food products isolated from 2000 to 2007 were analyzed by using antimicrobial agent, organic solvent, and disinfectant susceptibility tests, isoelectric focusing, detection of resistance determinants, plasmid profiling, pulsed-field gel electrophoresis (PFGE), and hybridization experiments. These isolates were compared to an outgroup consisting of 24 S. Saintpaul isolates obtained from humans and chickens in Germany and from poultry and poultry products (including turkeys) in Netherlands. A common core resistance pattern was detected for 27 German turkey and turkey product isolates. This pattern included resistance (full or intermediate) to ampicillin, amoxicillin-clavulanic acid, gentamicin, kanamycin, nalidixic acid, streptomycin, spectinomycin, and sulfamethoxazole and intermediate resistance or decreased susceptibility to ciprofloxacin (MIC, 2 or 1 μg/ml, respectively) and several third-generation cephalosporins (including ceftiofur and cefoxitin [MIC, 4 to 2 and 16 to 2 μg/ml, respectively]). These isolates had the same core resistance genotype, with bla TEM-1, aadB, aadA2, sul1, a Ser83→Glu83 mutation in the gyrA gene, and a chromosomal class 1 integron carrying the aadB-aadA2 gene cassette. Their XbaI, BlnI, and combined XbaI-BlnI PFGE patterns revealed levels of genetic similarity of 93, 75, and 90%, respectively. This study revealed that a multiresistant S. Saintpaul clonal line is widespread in turkeys and turkey products in Germany and was also detected among German human fecal and Dutch poultry isolates.

Download Full-text