scholarly journals Effects of a Direct-Fed Microbial and Feedlot Pen Environmental Change on Phenotypic Resistance among Enterococci Isolated from Beef Cattle Feces

2021 ◽  
Author(s):  
Sarah A. Murray ◽  
Ashlyn C. Holbert ◽  
Keri N. Norman ◽  
Sara D. Lawhon ◽  
Jason E. Sawyer ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Beef Cattle ◽  
Resistance Genes ◽  
Enterococcus Faecium ◽  
Sequence Type ◽  
Whole Genome ◽  
Fecal Samples ◽  
Phenotypic Resistance ◽  
The Impact ◽  
Sequence Types

In two sequential replicates (n=90 and n=96 feedlot finisher cattle, respectively) we measured the impact of an Enterococcus faecium-based probiotic (DFM) and an altered feedlot pen environment on antimicrobial resistance among fecal enterococci in cattle fed (or, not fed) the macrolide tylosin. Diluted fecal samples were spiral-plated on plain and antibiotic-supplemented m-Enterococcus agar. In the first replicate, tylosin significantly (p<0.05) increased the relative quantity of erythromycin-resistant enterococci. This effect was diminished in cattle fed the DFM in conjunction with tylosin. A similar observed effect was not statistically significant (P > 0.05) in the second replicate. Isolates were speciated and resistance phenotypes were obtained for E. faecium and E. hirae. E. faecium isolates were whole-genome sequenced, which yielded sequence types (ST), resistance genes and phylogeny. Samples of the DFM were sequenced and found to contain E. faecium ST296, which was not present on Day 0 of either replicate. This DFM sequence type was found in fecal samples after Day 0, the majority of which were isolated from cattle in one of the DFM-fed pens. Increased prevalence of ST296 occurred with a concomitant decrease in ST240; of importance, the latter typically harbored both ermB and tet(M) genes.

scholarly journals Effects of Tylosin, a Direct-Fed Microbial and Feedlot Pen Environment on Phenotypic Resistance among Enterococci Isolated from Beef Cattle Feces

Antibiotics ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 106
Author(s):  
Sarah A. Murray ◽  
Ashlyn C. Holbert ◽  
Keri N. Norman ◽  
Sara D. Lawhon ◽  
Jason E. Sawyer ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Beef Cattle ◽  
Enterococcus Faecium ◽  
Antibiotic Use ◽  
Fecal Samples ◽  
Phenotypic Resistance ◽  
Cattle Feces ◽  
The Impact ◽  
Selective Effects

In two sequential replicates (n = 90 and n = 96 feedlot finisher cattle, respectively) we measured the impact of an Enterococcus faecium-based probiotic (DFM) and an altered feedlot pen environment on antimicrobial resistance among fecal enterococci in cattle fed (or, not fed) the macrolide tylosin. Diluted fecal samples were spiral-plated on plain and antibiotic-supplemented m-Enterococcus agar. In the first replicate, tylosin significantly (p < 0.05) increased the relative quantity of erythromycin-resistant enterococci. This effect was diminished in cattle fed the DFM in conjunction with tylosin, indicating a macrolide susceptible probiotic may help mitigate resistance. A similar observed effect was not statistically significant (p > 0.05) in the second replicate. Isolates were speciated and resistance phenotypes were obtained for E. faecium and E. hirae. Susceptible strains of bacteria fed as DFM may prove useful for mitigating the selective effects of antibiotic use; however, the longer-term sustainability of such an approach remains unclear.

scholarly journals Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1152
Author(s):  
Samuel M. Chekabab ◽  
John R. Lawrence ◽  
Alvin C. Alvarado ◽  
Bernardo Z. Predicala ◽  
Darren R. Korber
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fecal Samples ◽  
Time Points ◽  
Conventional Farms ◽  
Production Practices ◽  
On Farm ◽  
The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

scholarly journals Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244358
Author(s):  
Rafika Indah Paramita ◽  
Erni Juwita Nelwan ◽  
Fadilah Fadilah ◽  
Editha Renesteen ◽  
Nelly Puspandari ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Virulence Genes ◽  
Sequence Type ◽  
Whole Genome ◽  
National Hospital ◽  
Sequence Types

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

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 Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Liseth Salinas ◽  
Paúl Cárdenas ◽  
Timothy J. Johnson ◽  
Karla Vasco ◽  
Jay Graham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Domestic Animals ◽  
Whole Genome ◽  
Content Type ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community. IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.

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 Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals 679. Predominance of Acinetobacter baumannii Sequence Type 2 (ST2) among Clinical Isolates from Two Detroit Hospitals using Whole Genome Sequencing

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S392-S393
Author(s):  
Piyali Chatterjee ◽  
Chetan Jinadatha ◽  
Keith S Kaye ◽  
Hosoon Choi ◽  
Yonhui Allton ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Minimum Spanning Tree ◽  
Veterans Affairs ◽  
Sequence Type ◽  
Whole Genome ◽  
Healthcare Associated Infections ◽  
Department Of Veterans Affairs ◽  
Healthcare Associated ◽  
Sequence Types ◽  
Research Grant

Abstract Background Healthcare-associated infections (HAIs) caused by Acinetobacter baumannii, an opportunistic gram-negative pathogen, often contribute to morbidity and mortality among hospitalized patients. To determine molecular epidemiology of circulating hospital Acinetobacter strains in Detroit area in a non-outbreak situation, we performed whole genome sequencing (WGS) and whole genome multilocus sequence typing (wgMLST) analysis to characterize genomic diversity. Methods We performed WGS on patient isolates from two disparate, geographically distinct tertiary care Detroit hospitals admitted to 16 intensive care units (ICU) and non-ICU wards between 2017-2019. The samples were obtained 48 hours following admission and WGS was performed using the Illumina NextSeq instrument. The contigs were de novo assembled using SPAdes and WgMLST analysis was performed using BioNumerics software v7.6. Minimum spanning tree (MST) was constructed to demonstrate the clusters in each hospital and their wards. Results WgMLST analysis was performed on a total of 62 Acinetobacter baumannii patient isolates, 33 of which were from hospital # 1 (H1) and 29 were from hospital # 2 (H2). ST2 (52%) was the predominant sequence type for both hospitals. In addition to ST2, ST93 (8%) and ST406 (8%) clusters were also found in H1. Most of the isolates were predominantly clustered in the intensive care unit (ICU) setting. Several identical sequence types of ST93 (2 identical in H1), ST36 (2 identical in H1) and ST2 (5 identical for H1 and 2 identical for H2) were also observed from different patients in both hospitals. Unlike H1, H2 only has ST2 as a predominant cluster. Other sporadic sequence types such as ST119, ST36, ST49, ST212, ST667 for H1 and ST395, ST214, ST427 and ST268 for H2 were also observed. Figure 1. MInimum Spanning Tree of Acinetobacter strains in hospitals (H1 and H2) and different wards (U1-U12). For identical strains circles are marked with dividing lines. Different sequence types (STs) are marked om the side bar. Conclusion Our data suggests that ST2 is the predominant sequence type circulating in both the geographically distinct hospitals and is endemic to the ICU. There was in hospital spread of this distinct Acinetobacter sequence type from one patient to the other, raising concerns about infection control practices and the role of environment in the spread of these infections. Early detection of these endemic strains within the hospital may be critical in preventing healthcare-associated infections in the future. Disclosures Chetan Jinadatha, MD, MPH, AHRQ (Research Grant or Support)Department of Veterans Affairs (Other Financial or Material Support, Owner: Department of Veterans Affairs. Licensed to: Xenex Disinfection System, San Antonio, TX)Inventor (Other Financial or Material Support, Methods for organizing the disinfection of one or more items contaminated with biological agents)NiH/NINR (Research Grant or Support)NSF (Research Grant or Support)Xenex Healthcare Services (Research Grant or Support) Mark Stibich, PhD MHS, Xenex Disinfection Services, Inc (Board Member, Employee)

scholarly journals WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Gamal Wareth ◽  
Christian Brandt ◽  
Lisa D. Sprague ◽  
Heinrich Neubauer ◽  
Mathias W. Pletz
Keyword(s):  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Acquired Resistance ◽  
Whole Genome ◽  
Chromosomal Gene ◽  
Milk Samples ◽  
Carbapenemase Gene

Abstract Background Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated. Results In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by blaADC.25 (38.6%) conferring resistance to cephalosporin, blaOXA-23 (29%) and the blaOXA-66 variant of the intrinsic blaOXA-51-likes (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. blaTEM variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic blaOXA-51 carbapenemase gene, blaOXA-510 and blaADC-25 genes were found in isolates obtained from dried milk samples. Conclusion The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.

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