scholarly journals Prevalence and Genetic Analysis of Chromosomal mcr-3/7 in Aeromonas From U.S. Animal-Derived Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Wang ◽  
Naxin Hou ◽  
Reuven Rasooly ◽  
Yongqiang Gu ◽  
Xiaohua He
Keyword(s):  
Resistance Genes ◽  
Lipid A ◽  
Housekeeping Genes ◽  
Domestic Animal ◽  
Broth Culture ◽  
Transferase Gene ◽  
Antimicrobial Resistance Genes ◽  
Meat Samples ◽  
Inspection Service ◽  
Pcr Targeting

The prevalence of mcr-positive bacteria in 5,169 domestic animal-derived samples collected by USDA Food Safety and Inspection Service between October 2018 and May 2019 was investigated. A procedure including enriched broth culture and real-time PCR targeting mcr-1 to mcr-8 were used for the screening. Fifteen positive isolates were identified, including one plasmid-borne mcr-1-positive Escherichia coli strain, EC2492 (reported elsewhere) and 14 mcr-3/7-positive strains from poultry (1), catfish (2), and chicken rinse (11) samples, resulting in an overall prevalence of mcr-positive bacteria 0.29% in all meat samples tested. Analysis of 16S rRNA and whole genome sequences revealed that all 14 strains belonged to Aeromonas. Data from phylogenetic analysis of seven housekeeping genes, including gyrB, rpoD, gyrA, recA, dnaJ, dnaX, and atpD, indicated that nine strains belonged to Aeromonas hydrophila and five strains belonged to Aeromonas jandaei. Antimicrobial tests showed that almost all mcr-positive strains exhibited high resistance to colistin with MICs ≥ 128mg/L, except for one A. jandaei strain, which showed a borderline resistance with a MIC of 2 mg/L. A segment containing two adjacent mcr-3 and mcr-3-like genes was found in two A. hydrophila and one A. jandaei strains and a variety of IS-like elements were found in the flanking regions of this segment. A mcr-3-related lipid A phosphoethanolamine transferase gene was present in all 14 Aeromonas strains, while an additional mcr-7-related lipid A phosphoethanolamine transferase gene was found in 5 A. jandaei strains only. In addition to mcr genes, other antimicrobial resistance genes, including blaOXA–12/OXA–724, aqu-2, tru-1, cepS, cphA, imiH, ceph-A3, ant(3″)-IIa, aac(3)-Via, and sul1 were observed in chromosomes of some Aeromonas strains. The relative high prevalence of chromosome-borne mcr-3/7 genes and the close proximity of various IS elements to these genes highlights the need for continued vigilance to reduce the mobility of these colistin-resistance genes among food animals.

scholarly journals  Molecular detection of antimicrobial resistance genes in E. coli isolated from slaughtered commercial chickens in Iran

2012 ◽  
Vol 57 (No. 4) ◽  
pp. 193-197 ◽  
Author(s):  
H. Momtaz ◽  
E. Rahimi ◽  
S. Moshkelani
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Molecular Detection ◽  
Antimicrobial Agents ◽  
Antibiotic Resistance Genes ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Meat Samples ◽  
Commercial Chickens

This study was carried out to detect the distribution of antibiotic-resistant genes in Escherichia coli isolates from slaughtered commercial chickens in Iran by PCR. The investigated genes included aadA1, tet(A), tet(B), dfrA1, qnrA, aac(3)-IV, sul1, bla<sub>SHV</sub>, bla<sub>CMY</sub>, ere(A), catA1 and cmlA. According to biochemical experiments, 57 isolates from 360 chicken meat samples were recognized as E. coli. The distribution of antibiotic-resistance genes in the E. coli isolates included tet(A) and tet(B) (52.63%), dfrA1, qnrA, catA1 and cmlA (36.84%) and sul1 and ere(A) (47.36%), respectively. Nine strains (15.78%) were resistant to a single antimicrobial agent and 11 strains (19.29%) showed resistance to two antimicrobial agents. Multi-resistance which was defined as resistance to three or more tested agents was found in 64.91% of E. coli strains. The results indicate that all isolates harbour one or more of antibiotic resistance genes and that the PCR technique is a fast, practical and appropriate method for determining the presence of antibiotic-resistance genes. &nbsp;

scholarly journals Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

2019 ◽  
Author(s):  
Leon Peto ◽  
Nicola J. Fawcett ◽  
Derrick W. Crook ◽  
Tim E.A. Peto ◽  
Martin J. Llewelyn ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Limit Of Detection ◽  
Broth Culture ◽  
Metagenomic Sequencing ◽  
Extended Spectrum Beta Lactamase ◽  
Antimicrobial Resistance Genes ◽  
Short Period ◽  
Culture Enrichment ◽  
Plasmid Extraction ◽  
Accurate Quantification

ABSTRACTMetagenomic sequencing of faecal DNA can usefully characterise an individual’s intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producingEnterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes inEnterobacteriaceaeby using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer faeces were spiked with carbapenemase-producingEnterobacteriaceaeand incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction protocols increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a faecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.

Antimicrobial Resistance Genes in Escherichia coli Isolates Recovered from a Commercial Beef Processing Plant†

2009 ◽  
Vol 72 (5) ◽  
pp. 1089-1093 ◽  
Author(s):  
MUEEN ASLAM ◽  
MOUSSA S. DIARRA ◽  
CARA SERVICE ◽  
HEIDI REMPEL
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Resistant Bacteria ◽  
Processing Plant ◽  
Ground Meat ◽  
E Coli ◽  
Beef Processing ◽  
Antimicrobial Resistance Genes ◽  
Meat Samples

The goal of this study was to assess the distribution of antimicrobial resistance (AMR) genes in Escherichia coli isolates recovered from a commercial beef processing plant. A total of 123 antimicrobial-resistant E. coli isolates were used: 34 from animal hides, 10 from washed carcasses, 27 from conveyers for moving carcasses and meat, 26 from beef trimmings, and 26 from ground meat. The AMR genes for β-lactamase (blaCMY, blaSHV, and blaTEM), tetracycline (tet(A), tet(B), and tet(C)), sulfonamides (sul1, sul2, and sul3), and aminoglycoside (strA and strB) were detected by PCR assay. The distribution of tet(B), tet(C), sul1, blaTEM, strA, and strB genes was significantly different among sample sources. E. coli isolates positive for the tet(B) gene and for both strA and strB genes together were significantly associated with hide, washed carcass, and ground meat samples, whereas sul1 gene was associated with washed carcass and beef trimming samples. The blaTEM gene was significantly associated with ground meat samples. About 50% of tetracycline-resistant E. coli isolates were positive for tet(A) (14%), tet(B) (15%), or tet(C) (21%) genes or both tet(B) and tet(C) genes together (3%). The sul2 gene or both sul1 and sul2 genes were found in 23% of sulfisoxazole-resistant E. coli isolates, whereas the sul3 gene was not found in any of the E. coli isolates tested. The majority of streptomycin-resistant E. coli isolates (76%) were positive for the strA and strB genes together. The blaCMY, blaTEM, and blaSHV genes were found in 12, 56, and 4%, respectively, of ampicillin-resistant E. coli isolates. These data suggest that E. coli isolates harboring AMR genes are widely distributed in meat processing environments and can create a pool of transferable resistance genes for pathogens. The results of this study underscore the need for effective hygienic and sanitation procedures in meat plants to reduce the risks of contamination with antimicrobial-resistant bacteria.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

scholarly journals The First Report of a Methicillin-Resistant Staphylococcus aureus Isolate Harboring Type IV SCCmec in Thailand

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 430
Author(s):  
Wichai Santimaleeworagun ◽  
Praewdow Preechachuawong ◽  
Wandee Samret ◽  
Tossawan Jitwasinkul
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Sccmec Type ◽  
Clinical Strain ◽  
Spa Typing ◽  
Methicillin Resistant ◽  
Type Iv ◽  
Antimicrobial Resistance Genes

Methicillin-resistant Staphylococcus aureus (MRSA) is mostly found in Thailand in the hospital as a nosocomial pathogen. This study aimed to report the genetic characterization of a clinical community-acquired MRSA (CA-MRSA) isolate collected from hospitalized patients in Thailand. Among 26 MRSA isolates, S. aureus no. S17 preliminarily displayed the presence of a staphylococcal cassette chromosome mec (SCCmec) type IV pattern. The bacterial genomic DNA was subjected to whole-genome sequencing. Panton–Valentine leukocidin (PVL) production, virulence toxins, and antibiotic resistance genes were identified, and multi-locus sequence typing (MLST) and spa typing were performed. The strain was matched by sequence to MLST type 2885 and spa type t13880. This strain carried type IV SCCmec with no PVL production. Five acquired antimicrobial resistance genes, namely blaZ, mecA, Inu(A), tet(K), and dfrG conferring resistance to β-lactams, lincosamides, tetracycline, and trimethoprim, were identified. The detected toxins were exfoliative toxin A, gamma-hemolysin, leukocidin D, and leukocidin E. Moreover, there were differences in seven regions in CR-MRSA no. S17 compared to CA-MRSA type 300. In summary, we have reported the ST2885-SCCmec IV CA-MRSA clinical strain in Thailand for the first time, highlighting the problem of methicillin resistance in community settings and the consideration in choosing appropriate antibiotic therapy.

Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia

2021 ◽  
Vol 194 ◽  
pp. 110730
Author(s):  
Olivia Ginn ◽  
Dennis Nichols ◽  
Lucas Rocha-Melogno ◽  
Aaron Bivins ◽  
David Berendes ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Surface Waters ◽  
Urban Surface ◽  
La Paz ◽  
Antimicrobial Resistance Genes
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