Horizontal Dissemination of Antimicrobial Resistance Determinants in Multiple Salmonella Serotypes following Isolation from the Commercial Swine Operation Environment after Manure Application

ABSTRACT The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farm environment after manure application on land. Manure and soil samples were collected on day 0 before and after manure application on six farms in North Carolina, and sequential soil samples were recollected on days 7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella, and their plasmid contents were further characterized. A total of 14 isolates including Salmonella enterica serotypes Johannesburg (n = 2), Ohio (n = 2), Rissen (n = 1), Typhimurium var5− (n = 5), Worthington (n = 3), and 4,12:i:− (n = 1), representing different farms, were selected for plasmid analysis. Antimicrobial susceptibility testing was done by broth microdilution against a panel of 14 antimicrobials on the 14 confirmed transconjugants after conjugation assays. The plasmids were isolated by modified alkaline lysis, and PCRs were performed on purified plasmid DNA to identify the AMR determinants and the plasmid replicon types. The plasmids were sequenced for further analysis and to compare profiles and create phylogenetic trees. A class 1 integron with an ANT(2″)-Ia-aadA2 cassette was detected in the 50-kb IncN plasmids identified in S. Worthington isolates. We identified 100-kb and 90-kb IncI1 plasmids in S. Johannesburg and S. Rissen isolates carrying the bla CMY-2 and tet(A) genes, respectively. An identical 95-kb IncF plasmid was widely disseminated among the different serotypes and across different farms. Our study provides evidence on the importance of horizontal dissemination of resistance determinants through plasmids of multiple Salmonella serotypes distributed across commercial swine farms after manure application. IMPORTANCE The horizontal gene transfer of antimicrobial resistance (AMR) determinants located on plasmids is considered to be the main reason for the rapid proliferation and spread of drug resistance. The deposition of manure generated in swine production systems into the environment is identified as a potential source of AMR dissemination. In this study, AMR gene-carrying plasmids were detected in multiple Salmonella serotypes across different commercial swine farms in North Carolina. The plasmid profiles were characterized based on Salmonella serotype donors and incompatibility (Inc) groups. We found that different Inc plasmids showed evidence of AMR gene transfer in multiple Salmonella serotypes. We detected an identical 95-kb plasmid that was widely distributed across swine farms in North Carolina. These conjugable resistance plasmids were able to persist on land after swine manure application. Our study provides strong evidence of AMR determinant dissemination present in plasmids of multiple Salmonella serotypes in the environment after manure application.

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Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018

mSphere ◽

10.1128/msphere.00161-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Lang Yang ◽

Bing Lü ◽

Quanyi Wang ◽

Kaiying Wang ◽

Yanfeng Lin ◽

...

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Bacillary Dysentery ◽

Shigella Flexneri ◽

Content Type ◽

Phylogenetic Characterization ◽

Local Expansion ◽

Resistance Determinants ◽

Genetic Features ◽

Beijing China

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.

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Complete Genome Sequence of Acinetobacter radioresistens Strain LH6, a Multidrug-Resistant Bacteriophage-Propagating Strain

Microbiology Resource Announcements ◽

10.1128/mra.00929-18 ◽

2018 ◽

Vol 7 (5) ◽

Cited By ~ 2

Author(s):

Clay S. Crippen ◽

Steven Huynh ◽

William G. Miller ◽

Craig T. Parker ◽

Christine M. Szymanski

Keyword(s):

Antimicrobial Resistance ◽

Acinetobacter Baumannii ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Related Species ◽

Complete Genome ◽

Multidrug Resistant ◽

Drug Resistant ◽

Content Type ◽

Resistance Determinants

Antimicrobial resistance is a major problem worldwide. Understanding the interplay between drug-resistant pathogens, such as Acinetobacter baumannii and related species, potentially acting as environmental reservoirs is critical for preventing the spread of resistance determinants.

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Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Dublin Isolates

Microbiology Resource Announcements ◽

10.1128/mra.00698-19 ◽

2019 ◽

Vol 8 (31) ◽

Author(s):

Baha Abdalhamid ◽

Emily L. Mccutchen ◽

Kacie D. Flaherty ◽

Steven H. Hinrichs ◽

Peter C. Iwen

Keyword(s):

Antimicrobial Resistance ◽

Salmonella Enterica ◽

Draft Genome ◽

Multidrug Resistant ◽

Genome Sequences ◽

Content Type ◽

Resistance Determinants ◽

Human Samples ◽

Systemic Infections ◽

Salmonella Enterica Serovar Dublin

Salmonella enterica serovar Dublin, which can cause enteritis and systemic infections in humans, has been associated with antimicrobial resistance. Here, we report draft genome sequences of seven multidrug-resistant S. Dublin isolates from human samples. These sequences will contribute to an understanding of pathogenesis and resistance determinants in this serovar.

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Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

Journal of Clinical Microbiology ◽

10.1128/jcm.00100-17 ◽

2017 ◽

Vol 55 (5) ◽

pp. 1454-1468 ◽

Cited By ~ 73

Author(s):

W. Demczuk ◽

S. Sidhu ◽

M. Unemo ◽

D. M. Whiley ◽

V. G. Allen ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Dna Sequences ◽

Diversity Index ◽

23S Rrna ◽

Content Type ◽

Typing Scheme ◽

Resistance Determinants ◽

Index Value ◽

User Friendly

ABSTRACTA curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants inNeisseria gonorrhoeaewas developed and is publicly accessible (https://ngstar.canada.ca). TheN. gonorrhoeaeSequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA,mtrR,porB,ponA,gyrA,parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entirepenAsequence, combining the historical nomenclature forpenAtypes I to XXXVIII with novel nucleotide sequence designations; the fullmtrRsequence and a portion of its promoter region; portions ofponA,porB,gyrA, andparC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n= 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n= 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n= 100; 13.0%), ST-42 and ST-91 (n= 45; 5.9%), ST-64 (n= 44; 5.72%), and ST-139 (n= 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n= 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n= 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n= 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n= 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistantN. gonorrhoeaestrains.

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Equations To Predict Antimicrobial MICs in Neisseria gonorrhoeae Using Molecular Antimicrobial Resistance Determinants

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02005-19 ◽

2019 ◽

Vol 64 (3) ◽

Cited By ~ 8

Author(s):

Walter Demczuk ◽

Irene Martin ◽

Pam Sawatzky ◽

Vanessa Allen ◽

Brigitte Lefebvre ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Training Data ◽

Sequencing Analysis ◽

Regression Equations ◽

Validation Data ◽

Data Set ◽

Content Type ◽

Resistance Determinants ◽

Extended Spectrum

ABSTRACT The emergence of Neisseria gonorrhoeae strains that are resistant to azithromycin and extended-spectrum cephalosporins represents a public health threat, that of untreatable gonorrhea infections. Multivariate regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to the overall antimicrobial MICs for ceftriaxone, cefixime, azithromycin, tetracycline, ciprofloxacin, and penicillin. A training data set consisting of 1,280 N. gonorrhoeae strains was used to generate regression equations which were then applied to validation data sets of Canadian (n = 1,095) and international (n = 431) strains. The predicted MICs for extended-spectrum cephalosporins (ceftriaxone and cefixime) were fully explained by 5 amino acid substitutions in PenA, A311V, A501P/T/V, N513Y, A517G, and G543S; the presence of a disrupted mtrR promoter; and the PorB G120 and PonA L421P mutations. The correlation of predicted MICs within one doubling dilution to phenotypically determined MICs of the Canadian validation data set was 95.0% for ceftriaxone, 95.6% for cefixime, 91.4% for azithromycin, 98.2% for tetracycline, 90.4% for ciprofloxacin, and 92.3% for penicillin, with an overall sensitivity of 99.9% and specificity of 97.1%. The correlations of predicted MIC values to the phenotypically determined MICs were similar to those from phenotype MIC-only comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular data will facilitate the transition to whole-genome sequencing analysis from phenotypic testing and can fill the surveillance gap in an era of increased reliance on nucleic acid assay testing (NAAT) diagnostics to better monitor the dynamics of N. gonorrhoeae.

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Genetic relatedness of Streptococcus dysgalactiae isolates causing recurrent bacteraemia

Journal of Medical Microbiology ◽

10.1099/jmm.0.001330 ◽

2021 ◽

Author(s):

Erik Senneby ◽

Björn Hallström ◽

Magnus Rasmussen

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Trees ◽

Genetic Relatedness ◽

Sequence Similarity ◽

Streptococcus Dysgalactiae ◽

High Sequence Similarity ◽

Content Type ◽

Link Type ◽

Clonal Origin

Introduction. Streptococcus dysgalactiae subspecies equisimilis (SDSE) is becoming increasingly recognized as an important human pathogen. Recurrent bacteremia with SDSE has been described previously. Aim. The aims of the study were to establish the genetic relatedness of SDSE isolates with emm-type stG643 that had caused recurrent bacteraemia in three patients and to search for signs of horizontal gene transfer of the emm gene in a collection of SDSE stG643 genomes. Hypothesis. Recurring SDSE bacteremia is caused by the same clone in one patient. Methodology. Whole genome sequencing of 22 clinical SDSE stG643 isolates was performed, including three paired blood culture isolates and sixteen isolates from various sites. All assemblies were aligned to a reference assembly and SNPs were extracted. A total of 53 SDSE genomes were downloaded from GenBank. Two phylogenetic trees, including all 75 SDSE isolates, were created. One tree was based on the emm gene only and one tree was based on all variable positions in the genomes. Results. The genomes from the three pairs of SDSE isolates showed high sequence similarity (1–17 SNPs difference between the pairs), whereas the median SNP difference between the 22 isolates in our collection was 1694 (range 1–11257). The paired isolates were retrieved with 7–53 months between episodes. The 22 SDSE isolates from our collection formed a cluster in the phylogenetic tree based on the emm gene, while they were more scattered in the tree based on all variable positions. Conclusions. Our results show that the paired isolates were of the same clonal origin, which in turn supports carriage between bacteraemia episodes. The phylogenetic analysis indicates that horizontal gene transfer of the emm-gene between some of the SDSE isolates has occurred.

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Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01950-15 ◽

2016 ◽

Vol 60 (5) ◽

pp. 2972-2980 ◽

Cited By ~ 43

Author(s):

Masato Akiba ◽

Tsuyoshi Sekizuka ◽

Akifumi Yamashita ◽

Makoto Kuroda ◽

Yuki Fujii ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Sewage Treatment ◽

Indian States ◽

Content Type ◽

Sewage Treatment Plants ◽

E Coli ◽

Resistance Determinants ◽

Carbapenem Resistant ◽

Extended Spectrum

ABSTRACTTo determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistantEscherichia coliisolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446E. coliisolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%)E. coliisolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. TheblaNDMgene was detected in 14/21 carbapenem-resistantE. coliisolates:blaNDM-1in 2 isolates,blaNDM-5in 7 isolates, andblaNDM-7in 5 isolates. TheblaCTX-Mgene was detected in 112 isolates (66.3%):blaCTX-M-15in 108 isolates andblaCTX-M-55in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of theblaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.

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Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa

mBio ◽

10.1128/mbio.01603-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 47

Author(s):

Justine L. Murray ◽

Taejoon Kwon ◽

Edward M. Marcotte ◽

Marvin Whiteley

Keyword(s):

Gene Expression ◽

Pseudomonas Aeruginosa ◽

Antimicrobial Resistance ◽

Good Predictor ◽

Molecular Mechanisms ◽

Financial Burden ◽

Resistant Bacteria ◽

Intrinsic Resistance ◽

Content Type ◽

Resistance Determinants

ABSTRACT Antimicrobial-resistant bacteria pose a serious threat in the clinic. This is particularly true for opportunistic pathogens that possess high intrinsic resistance. Though many studies have focused on understanding the acquisition of bacterial resistance upon exposure to antimicrobials, the mechanisms controlling intrinsic resistance are not well understood. In this study, we subjected the model opportunistic superbug Pseudomonas aeruginosa to 14 antimicrobials under highly controlled conditions and assessed its response using expression- and fitness-based genomic approaches. Our results reveal that gene expression changes and mutant fitness in response to sub-MIC antimicrobials do not correlate on a genomewide scale, indicating that gene expression is not a good predictor of fitness determinants. In general, fewer fitness determinants were identified for antiseptics and disinfectants than for antibiotics. Analysis of gene expression and fitness data together allowed the prediction of antagonistic interactions between antimicrobials and insight into the molecular mechanisms controlling these interactions. IMPORTANCE Infections involving multidrug-resistant pathogens are difficult to treat because the therapeutic options are limited. These infections impose a significant financial burden on infected patients and on health care systems. Despite years of antimicrobial resistance research, we lack a comprehensive understanding of the intrinsic mechanisms controlling antimicrobial resistance. This work uses two fine-scale genomic approaches to identify genetic loci important for antimicrobial resistance of the opportunistic pathogen Pseudomonas aeruginosa. Our results reveal that antibiotics have more resistance determinants than antiseptics/disinfectants and that gene expression upon exposure to antimicrobials is not a good predictor of these resistance determinants. In addition, we show that when used together, genomewide gene expression and fitness profiling can provide mechanistic insights into multidrug resistance mechanisms.

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Prevalence of genotypic antimicrobial resistance in clinical Shiga toxin-producing Escherichia coli in Norway, 2018 to 2020

Journal of Medical Microbiology ◽

10.1099/jmm.0.001454 ◽

2021 ◽

Vol 70 (12) ◽

Author(s):

Silje N. Ramstad ◽

Lin T. Brandal ◽

Arne M. Taxt ◽

Yngvild Wasteson ◽

Jørgen V. Bjørnholt ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Shiga Toxin ◽

Antimicrobial Treatment ◽

Multi Drug Resistance ◽

Reference Laboratory ◽

Virulence Determinants ◽

Genotypic Resistance ◽

Content Type ◽

Resistance Determinants

Introduction. Shiga toxin-producing Escherichia coli (STEC) can cause severe to fatal disease in humans. Antimicrobial treatment is sometimes necessary, but contraindicated due to undesirable clinical outcome. However, recent studies have shown promising outcomes following antimicrobial treatment. Before the establishment of a possible antimicrobial treatment strategy for STEC infections, the prevalence of antimicrobial resistance in STEC needs to be determined. Gap Statement. The resistance status of Norwegian clinical STEC is not known and should be assessed. Aim. We aim to characterize genotypic antimicrobial resistance determinants in clinical STEC in Norway, and determine the prevalence of genotypic resistance in order to inform possible antimicrobial treatment options for STEC infections. Methodology. We included all clinical STEC submitted to the Norwegian Reference Laboratory from March 2018 to April 2020. All samples were whole-genome sequenced and screened for genotypic antimicrobial resistance,virulence determinants and plasmid incompatibility groups. We performed phylogenetic clustering of STEC by core-genome multi-locus sequence typing, and statistical association analyses between isolate characteristics and genotypic resistance. Results. A total of 459 STEC were analysed. For 385 (83.9 %) STEC we did not identify any antimicrobial resistance determinants. Seventy-four STEC (16.1 %) harboured antimicrobial resistance determinants against one or more antimicrobial classes. The most frequent genotypic resistance was identified against aminoglycosides (10.5 %). Thirty-nine STEC (8.5 %) had a multi-drug resistance (MDR) genotype. Genotypic resistance was more prevalent in non-O157 than O157 STEC (P=0.02). A positive association was seen between genotypic resistance and the low-virulent STEC O117:H7 phylogenetic cluster (no. 14) (P<0.001). Genotypic resistance was not significantly associated to high-virulent STEC. STEC O146:H28 and isolates harbouring the plasmid replicon type IncQ1 were positively associated with MDR. Conclusion. The overall prevalence of genotypic resistance in clinical STEC in Norway is low (16.1 %). Genotypic resistance is more prevalent in non-O157 strains compared to O157 strains, and not significantly associated to high-virulent STEC. Resistance to antimicrobials suggested for treatment, especially azithromycin is low and may present an empiric treatment alternative for severe STEC infections.

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