scholarly journals Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1131
Author(s):  
Noel Gahamanyi ◽  
Dae-Geun Song ◽  
Kye-Yoon Yoon ◽  
Leonard E. G. Mboera ◽  
Mecky I. Matee ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Coli Strain ◽  
Whole Genome ◽  
Thermophilic Campylobacter ◽  
Antimicrobial Resistance Genes ◽  
Campylobacter Species

Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the presence of selected antimicrobial resistance genes was performed by polymerase chain reaction (PCR) using specific primers. Whole-genome sequencing (WGS) was performed by the Illumina HiSeq X platform. The analysis involved antimicrobial resistance genes, virulome, multilocus sequence typing (MLST), and phylogeny. Both isolates were phenotypically resistant to ciprofloxacin (MIC: 32 vs. 32 µg/mL), nalidixic acid (MIC: 128 vs. 64 µg/mL), and tetracycline (MIC: 64 vs. 64 µg/mL), but sensitive to erythromycin (MIC: 1 vs. 2 µg/mL) and gentamicin (MIC: 0.25 vs. 1 µg/mL) for C. jejuni strain 200605 and C. coli strain 200606, respectively. WGS confirmed C257T mutation in the gyrA gene and the presence of cmeABC complex conferring resistance to FQs in both strains. Both strains also exhibited tet(O) genes associated with tetracycline resistance. Various virulence genes associated with motility, chemotaxis, and capsule formation were found in both isolates. However, the analysis of virulence genes showed that C. jejuni strain 200605 is more virulent than C. coli strain 200606. The MLST showed that C. jejuni strain 200605 belongs to sequence type ST-5229 while C. coli strain 200606 belongs to ST-5935, and both STs are less common. The phylogenetic analysis clustered C. jejuni strain 200605 along with other strains reported in Korea (CP028933 from chicken and CP014344 from human) while C. coli strain 200606 formed a separate cluster with C. coli (CP007181) from turkey. The WGS confirmed FQ-resistance in both strains and showed potential virulence of both strains. Further studies are recommended to understand the reasons behind the regional distribution (Korea, China, and Vietnam) of such rare STs.

scholarly journals Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

2020 ◽  
Vol 11 ◽  
Author(s):  
Grazielle Lima Rodrigues ◽  
Pedro Panzenhagen ◽  
Rafaela Gomes Ferrari ◽  
Anamaria dos Santos ◽  
Vania Margaret Flosi Paschoalin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes

scholarly journals Genomic Characterization of Multidrug-Resistant Carbapenemase-Producing Enterobacter cloacae ECL189, Co-producing KPC-2, NDM-1, TEM-1, TEM-95, and SHV-66

2021 ◽  
Vol 13 (11) ◽  
Author(s):  
Na Du ◽  
Shumin Liu ◽  
Jing Yao ◽  
Kai Yang ◽  
Yun Lin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Enterobacter Cloacae ◽  
Biological Information ◽  
Whole Genome ◽  
Carbapenem Resistant ◽  
Transmission Mechanisms ◽  
Antimicrobial Resistance Genes

Background: Carbapenem-resistant Enterobacteriaceae (CRE) has become a public health threat due to resistance to multiple antibiotics. The production of β-lactamase is the most important resistance mechanism of Enterobacteriaceae. Although isolates producing KPC-2 or NDM-1 enzymes have been reported widely, isolates co-producing KPC-2, NDM-1, TEM-1, TEM-95, SHV-66, and other β-lactamases have rarely been detected in the same strain, especially in Enterobacter cloacae. Objectives: In this study, we identified and sequenced the genome of carbapenem-resistant E. cloacae ECL189 to in-depth analyze the resistance and transmission mechanisms of E. cloacae. Methods: We investigated the antimicrobial susceptibility of ECL189 by a VITEK 2 system, E-test gradient strips, and K-B method. Whole-genome sequencing was used by the PacBio RS II platform and Illumina HiSeq 4000 platform. Antimicrobial resistance genes, virulence genes, non-coding RNA, and repeat sequences were predicted by biological information databases. A PCR was used to further confirm that the blaKPC-2, blaNDM-1, blaTEM-1, blaTEM-95, and blaSHV-66 genes existed in ECL189. A conjugation experiment was performed to determine the transferability of resistance. Molecular typing of ECL189 was done by multilocus sequence typing (MLST). Results: Enterobacter cloacae ECL189 was resistant to 21 out of 23 tested antibiotics, but its transconjugant was resistant to 10 out of 18 tested antibiotics. The genome of ECL189 consisted of a 5,026,406 bp chromosome and four circular plasmids. In total, 26 resistance genes and 58 resistance proteins were identified. In addition, 77 determinants associated with bacterial virulence were identified. A large number of resistance and virulence genes were located in the plasmids. The results of whole-genome sequencing were consistent with the β-lactamase genes. The MLST analysis revealed that this strain belonged to ST74. Conclusions: This study further revealed the resistance, virulence, and transmission mechanisms of carbapenem-resistant E. cloacae. Resistance and virulence genes spread in bacteria by the horizontal transfer of plasmids, which should attract more attention in relevant departments.

scholarly journals Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella Aerogenes

2020 ◽  
Author(s):  
Fang Huang ◽  
Shuang Li ◽  
Xiaohui Chi ◽  
Peipei Wen ◽  
Hao Fu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Klebsiella Aerogenes ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

Abstract Background: Bronchoscopes has been linked to the outbreaks of nosocomial infections. We aim to investigate the phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates, and their association with genome public available isolates from human and environment.Methods: We performed a prospective single-center study sampling echoendoscopes after clinical use and after normal decontamination procedures. Bacterial screening was conducted by culturing the sample on Mueller-Hinton agar plates. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing of K. aerogenes isolates was performed using an Illumina HiSeq system and comparative genomics analysis were conducted.Results: Over the 5-month period, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively. Antimicrobial susceptibility testing found 7 K. aerogenes isolates to exhibit low-level resistance to antimicrobial agents. Among 7 K. aerogenes isolates, we found 5 sequence types (STs). Whole genome sequencing and comparison analysis observed the genetic diversity in our bacterial collection, which clustered into three main clades. Furthermore, we identified a total of 43 antimicrobial resistance genes in the K. aerogenes core genomes. As expected, human isolates encoded more antimicrobial resistance genes than that environmental isolates. Conclusions: This study first described the phenotypic and genomics characteristics of bronchoscope-associated K. aerogenes. The present observations demonstrated that broadly investigation of specific pathogens using publicly available global genomes offered the opportunity to identify prevalent clones associated with various hosts, sources, and geographical locations.

scholarly journals Comparison of Antimicrobial Resistance and Pan-Genome of Clinical and Non-Clinical Enterococcus cecorum from Poultry Using Whole-Genome Sequencing

Foods ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 686
Author(s):  
Poonam Sharma ◽  
Sushim K. Gupta ◽  
John B. Barrett ◽  
Lari M. Hiott ◽  
Tiffanie A. Woodley ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Gene Families ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Pan Genome ◽  
Antimicrobial Resistance Genes ◽  
Enterococcus Cecorum

Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol, suggesting possible new mechanisms of resistance to these drugs. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.

scholarly journals Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-associated Klebsiella aerogenes

2020 ◽  
Author(s):  
Fang Huang ◽  
Shuang Li ◽  
Xiaohui Chi ◽  
Peipei Wen ◽  
Hao Fu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Klebsiella Aerogenes ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

Abstract Background: Bronchoscopes has been linked to the outbreaks of nosocomial infections. We aim to investigate the phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates, and their association with genome public available isolates from human and environment.Methods: We performed a prospective single-center study sampling echoendoscopes after clinical use and after normal decontamination procedures. Bacterial screening was conducted by culturing the sample on Mueller-Hinton agar plates. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing of K. aerogenes isolates was performed using an Illumina HiSeq system and comparative genomics analysis were conducted.Results: Over the 5-month period, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively. Antimicrobial susceptibility testing found 7 K. aerogenes isolates to exhibit low-level resistance to antimicrobial agents. Among 7 K. aerogenes isolates, we found 5 sequence types (STs). Whole genome sequencing and comparison analysis observed the genetic diversity in our bacterial collection, which clustered into three main clades. Furthermore, we identified a total of 43 antimicrobial resistance genes in the K. aerogenes core genomes. As expected, human isolates encoded more antimicrobial resistance genes than that environmental isolates. Conclusions: This study first described the phenotypic and genomics characteristics of bronchoscope-associated K. aerogenes. The present observations demonstrated that broadly investigation of specific pathogens using publicly available global genomes offered the opportunity to identify prevalent clones associated with various hosts, sources, and geographical locations.

scholarly journals Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011-2019

2020 ◽  
Author(s):  
Justine Schaeffer ◽  
Steliana Huhulescu ◽  
Anna Stoeger ◽  
Franz Allerberger ◽  
Werner Ruppitsch
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Diphtheria Toxin ◽  
Corynebacterium Diphtheriae ◽  
Toxin Gene ◽  
Whole Genome ◽  
Skin Infections ◽  
Antimicrobial Resistance Genes

Background: Diphtheria is a vaccine preventable disease with a high potential for re-emergence. One of its causative agent is Corynebacterium diphtheriae, some strains producing the diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory track or from skin infections. Objectives: The aim of the study was to investigate the genetic diversity of these C. diphtheriae isolates using whole genome sequencing. Methods: Isolates were characterized by genome wide comparison using single nucleotide polymorphism or core genome multilocus sequence typing, and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. Results: Genetic diversity between the isolates was high, with no clear distribution over time or place. C. belfantii isolates were separated from other strains, and were strongly associated with respiratory infections (OR = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin, but did not carry genes conferring β-lactam resistance. Diphtheria toxin gene with no non-synonymous mutation was found in three isolates only. Conclusion: This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistances more broadly and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole genome sequencing.

scholarly journals Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex

2020 ◽  
Vol 86 (10) ◽  
Author(s):  
Mélanie Mercier-Darty ◽  
Guilhem Royer ◽  
Brigitte Lamy ◽  
Chadly Charron ◽  
Olivier Lemenand ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Stenotrophomonas Maltophilia ◽  
Whole Genome ◽  
Content Type ◽  
Genetic Organization ◽  
Animal Strains

ABSTRACT The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans. IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

Sign in / Sign up

Export Citation Format

Share Document