scholarly journals Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia: TABLE 1 

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Johan F. Bernal ◽  
Pilar Donado-Godoy ◽  
María Fernanda Valencia ◽  
Maribel León ◽  
Yolanda Gómez ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Monitoring Program ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Genome Sequences ◽  
Resistance Monitoring ◽  
Antimicrobial Resistance Genes

Campylobacter coli , along with Campylobacter jejuni , is a major agent of gastroenteritis and acute enterocolitis in humans. We report the whole-genome sequences of two multidrug-resistance C. coli strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline.

scholarly journals Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Medelin Ocejo ◽  
Beatriz Oporto ◽  
José Luis Lavín ◽  
Ana Hurtado
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Northern Spain ◽  
Sequence Alignments ◽  
Phenotypic Data ◽  
Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

scholarly journals Presence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food

2021 ◽  
Vol 11 ◽  
Author(s):  
Feng Zhang ◽  
Shi Wu ◽  
Jiahui Huang ◽  
Runshi Yang ◽  
Jumei Zhang ◽  
...  
Keyword(s):  
Public Health ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Poultry Meat ◽  
Whole Genome ◽  
Chloramphenicol Resistance ◽  
Antimicrobial Resistance Genes ◽  
Retail Food

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

scholarly journals Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Nesreen H. Aljahdali ◽  
Pravin R. Kaldhone ◽  
Steven L. Foley ◽  
Bijay K. Khajanchi
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Genome Sequences ◽  
Incompatibility Group ◽  
Content Type ◽  
Food Animal ◽  
Antimicrobial Resistance Genes ◽  
Genotypic Characteristics

We sequenced 35 Salmonella enterica isolates carrying incompatibility group I1 (IncI1) plasmids from different serotypes to study their genotypic characteristics. The isolates originated from food animals (n = 32) and human patients (n = 3). All isolates carried IncI1 plasmids, and many had additional plasmids detected along with virulence and antimicrobial resistance genes.

scholarly journals Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Vikrant Dutta ◽  
Eric Altermann ◽  
Jonathan Olson ◽  
Gregory Allan Wray ◽  
Robin M. Siletzky ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Multidrug Resistant ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Genome Sequences ◽  
Swine Feces

We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from turkey-house water and swine feces, respectively. The genomes provide insights on Campylobacter antimicrobial resistance and host adaptations.

scholarly journals Complete Genome Sequences of Multidrug-ResistantCampylobacter jejuniStrain 14980A (Turkey Feces) andCampylobacter coliStrain 14983A (Housefly from a Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
William G. Miller ◽  
Steven Huynh ◽  
Craig T. Parker ◽  
Jeffrey A. Niedermeyer ◽  
Sophia Kathariou
Keyword(s):  
Public Health ◽  
Multidrug Resistance ◽  
Campylobacter Jejuni ◽  
Foodborne Pathogens ◽  
Mobile Element ◽  
Public Health Issue ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Genome Sequences ◽  
Gentamicin Resistance

Multidrug resistance (MDR) in foodborne pathogens is a major food safety and public health issue. Here we describe whole-genome sequences of two MDR strains ofCampylobacter jejuniandCampylobacter colifrom turkey feces and a housefly from a turkey farm.Both strains harbor a novel chromosomal gentamicin resistance mobile element.

scholarly journals Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania

2020 ◽  
Vol 9 (1) ◽  
pp. 66
Author(s):  
Jurgita Aksomaitiene ◽  
Aleksandr Novoslavskij ◽  
Egle Kudirkiene ◽  
Ausra Gabinaitiene ◽  
Mindaugas Malakauskas
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Genome Sequences ◽  
Resistance Determinants ◽  
High Level

Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania.

scholarly journals Draft Whole-Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Senftenberg Sequence Type 14 Strains Resistant to Ciprofloxacin, Ceftriaxone, and/or Azithromycin, Isolated from Kolkata, India

2022 ◽  
Author(s):  
Priyanka Jain ◽  
Rajlakshmi Viswanathan ◽  
Gourab Halder ◽  
Sulagna Basu ◽  
Shanta Dutta
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Goat Meat ◽  
Antimicrobial Resistance Genes

We report draft whole-genome sequences of two multidrug-resistant Salmonella enterica serovar Senftenberg sequence type 14 strains resistant to ciprofloxacin, ceftriaxone, and/or azithromycin, which were isolated from neonatal stool and goat meat in Kolkata, India. The genome characteristics, as well as the antimicrobial resistance genes, plasmid types, and integrons, are presented in this report.

scholarly journals Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland

2021 ◽  
Vol 22 (17) ◽  
pp. 9381
Author(s):  
Tomasz Wołkowicz ◽  
Katarzyna Zacharczuk ◽  
Rafał Gierczyński ◽  
Magdalena Nowakowska ◽  
Katarzyna Piekarska
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Island ◽  
Test Methods ◽  
Whole Genome ◽  
Disc Diffusion ◽  
Genome Sequences ◽  
Antimicrobial Resistance Genes ◽  
High Level ◽  
Relationship Of

Background: Salmonella Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical S. Kentucky strains isolated in Poland remain undescribed. Methods: Eighteen clinical S. Kentucky strains collected in the years 2018–2019 in Poland were investigated. All the strains were tested for susceptibility to 11 antimicrobials using the disc diffusion and E-test methods. Whole genome sequences were analysed for antimicrobial resistance genes, mutations, the presence and structure of SGI1-K (Salmonella Genomic Island and the genetic relationship of the isolates. Results: Sixteen of 18 isolates (88.9%) were assigned as ST198 and were found to be high-level resistant to ampicillin (>256 mg/L) and quinolones (nalidixic acid MIC ≥ 1024 mg/L, ciprofloxacin MIC range 6–16 mg/L). All the 16 strains revealed three mutations in QRDR of GyrA and ParC. The substitutions of Ser83 → Phe and Asp87 → Tyr of the GyrA subunit and Ser80→Ile of the ParC subunit were the most common. One S. Kentucky isolate had qnrS1 in addition to the QRDR mutations. Five of the ST198 strains, grouped in cluster A, had multiple resistant determinants like blaTEM1-B, aac(6′)-Iaa, sul1 or tetA, mostly in SGI1 K. Seven strains, grouped in cluster B, had shorter SGI1-K with deletions of many regions and with few resistance genes detected. Conclusion: The results of this study demonstrated that a significant part of S. Kentucky isolates from humans in Poland belonged to ST198 and were high-level resistant to ampicillin and quinolones.

scholarly journals Isolation and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli found in chilled chicken carcasses in the Federal District Region and surrounding areas

2019 ◽  
Vol 40 (5Supl1) ◽  
pp. 2247
Author(s):  
Patricia Renault Silva ◽  
Joana Marchesini Palma ◽  
Nara Rubia Souza ◽  
Helenira Melo de Moura ◽  
Simone Perecmanis ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Federal District ◽  
Occurrence Rate ◽  
Campylobacter Coli ◽  
Antimicrobial Resistance Genes ◽  
Polymerase Chain ◽  
Surrounding Areas

This study aimed to isolate Campylobacter jejuni and Campylobacter coli from chilled chicken carcasses marketed in the Federal District Region and surrounding areas, as well as to detect the occurrence of antimicrobial resistance and genes responsible for the same. A total of 105 chilled chicken carcasses were collected, of which 7 (6.67%) were positive for C. jejuni and 4 (3.81%) were positive for C. coli. These results were obtained using both the conventional microbiological isolation method and polymerase chain reaction assays. All of the positive strains were subjected to antimicrobial susceptibility testing for seven antimicrobials. The resistance incidences found in the C. jejuni strains were as follows: 71.43% for tetracycline and nalidixic acid, 42.86% for streptomycin and gentamicin, 57.14% for ciprofloxacin and erythromycin, and 28.57% for chloramphenicol. Among the C. coli strains, 100% were resistant to tetracycline and streptomycin, 75% were resistant to erythromycin, 50% were resistant to ciprofloxacin, gentamicin, and nalidixic acid, and no strains were resistant to chloramphenicol. While analyzing the presence of antimicrobial resistance genes in the isolated C. jejuni strains, the aph3-1 (resistance to aminoglycosides), aadE (resistance to streptomycin), and tet(O) (resistance to tetracycline) genes were identified, with occurrence rates of 57.14%, 28.57%, and 42.86%, respectively, whereas in the C. coli strains, there was a 25% occurrence rate for both the aph3-1 and tet(O) genes. The aadE gene was not found in the C. coli isolates. The results of this study demonstrated the presence of C. jejuni and C. coli in chilled chicken carcasses marketed in the Federal District Region and surrounding areas, as well as the antimicrobial resistance and the presence of resistance genes in these bacteria, which may pose threats to public health.

scholarly journals Genomic Characterization of Multidrug-Resistant Salmonella Serovars Derby and Rissen From the Pig Value Chain in Vietnam

2021 ◽  
Vol 8 ◽  
Author(s):  
Belén González-Santamarina ◽  
Silvia García-Soto ◽  
Sinh Dang-Xuan ◽  
Mostafa Y. Abdel-Glil ◽  
Diana Meemken ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Value Chain ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Whole Genome ◽  
Bioinformatics Analyses ◽  
Antimicrobial Resistance Genes ◽  
Genomic Characterization

Nontyphoidal Salmonella (NTS) is the most reported cause of bacterial foodborne zoonoses in Vietnam, and contaminated pork is one of the main sources of human infection. In recent years, the prevalence of NTS carrying multiple antimicrobial resistance genes (ARGs) have been increased. The genomic characterization along the pig value chain and the identification of ARGs and plasmids have the potential to improve food safety by understanding the dissemination of ARGs from the farm to the table. We report an analysis of 13 S. Derby and 10 S. Rissen isolates, collected in 2013 at different stages in Vietnamese slaughterhouses and markets. VITEK 2 Compact System was used to characterize the phenotypical antimicrobial resistance of the isolates. In addition, whole-genome sequencing (WGS) was used to detect ARGs and plasmids conferring multidrug resistance. Whole genome single nucleotide polymorphism typing was used to determine the genetic diversity of the strains and the spread of ARGs along the pig value chain. Altogether, 86.9% (20/23) of the samples were resistant to at least one antibiotic. Resistance to ampicillin was most frequently detected (73.9%), followed by piperacillin and moxifloxacin (both 69.6%). At least one ARG was found in all strains, and 69.6% (16/23) were multidrug-resistant (MDR). The observed phenotype and genotype of antimicrobial resistance were not always concordant. Plasmid replicons were found in almost all strains [95.6% (22/23)], and the phylogenetic analysis detected nine clusters (S. Derby, n = 5; S. Rissen, n = 4). ARGs and plasmid content were almost identical within clusters. We found six MDR IncHI1s with identical plasmid sequence type in strains of different genetic clusters at the slaughterhouse and the market. In conclusion, high rates of multidrug resistance were observed in Salmonella strains from Vietnam in 2013. Genomic analysis revealed many resistance genes and plasmids, which have the potential to spread along the pig value chain from the slaughterhouse to the market. This study pointed out that bioinformatics analyses of WGS data are essential to detect, trace back, and control the MDR strains along the pig value chain. Further studies are necessary to assess the more recent MDR Salmonella strains spreading in Vietnam.

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