Antimicrobial Resistance Genes and Bacteria Detected in Hospital Sewage May Provide Valuable Information in Clinical Antimicrobial Resistance

Abstract Aim: Clinical antimicrobial resistance (AMR) is a significant threat to public health, which is often unclear due to representative data from human populations that are challenging to obtain. Study the associations between consumption of antibiotics and antimicrobial resistance bacteria or genes (ARB or ARGs) that will benefit from elucidating the AMR. Methods: The details of antibiotics usage were calculated based on the actual consumption in the target hospital, ARB was detected by culture method, and ARGs were evaluated by metagenomics. Results: Our study revealed that culture-based single-indicator-strain approaches only capture the AMR in 16.17% infectious samples. 1573 bacterial species and 885 types of ARGs were found in the hospital sewage. The consumption of antibiotics influences the resistance profiles that were significant in E.coli, but the strength varies among bacteria. In all ARGs group, ARGs of aminoglycosides was the most common, followed by sulfonamide, tetracycline, phenicol, macrolides, and quinolones, comprising to 82.6% of all ARGs. Five hundred nineteen pairs of ARGs and bacterial species showed a significant correlation (r > 0.8). The co-occurrence patterns of bacteria- ARGs mirrors the AMR of the clinic. Antibiotic usage will affect the abundance of ARG in sewage, with a hysteresis effect. Conclusion: The ARGs- bacteria co-occurrence patterns from wastewater could be a valuable bio-indicator to reflect the emergence of ARB in the future. Developing a predictive risk model of AMR on this basis will facilitate the rational use of antibiotics.

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Antimicrobial resistance genes in raw milk for human consumption

Scientific Reports ◽

10.1038/s41598-020-63675-4 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Adrienn Gréta Tóth ◽

István Csabai ◽

Eszter Krikó ◽

Dóra Tőzsér ◽

Gergely Maróti ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Species ◽

Raw Milk ◽

Human Consumption ◽

Human Populations ◽

Peptide Antibiotics ◽

Milk Samples ◽

Antimicrobial Resistance Genes ◽

Depth Analysis

AbstractThe increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.

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Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

Current Bioinformatics ◽

10.2174/1574893615999200608130029 ◽

2020 ◽

Vol 15 ◽

Author(s):

Akshatha Prasanna ◽

Vidya Niranjan

Keyword(s):

Antimicrobial Resistance ◽

High Performance ◽

Pathogen Detection ◽

Bacterial Species ◽

Workflow Management ◽

Metagenomic Data ◽

Antimicrobial Resistance Genes ◽

Culture Independent ◽

Automated Pipeline ◽

User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

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Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for FiveBacillusSpecies Relevant for Use as Animal Feed Additives or for Plant Protection

Applied and Environmental Microbiology ◽

10.1128/aem.01108-18 ◽

2018 ◽

Vol 84 (19) ◽

Cited By ~ 7

Author(s):

Yvonne Agersø ◽

Birgitte Stuer-Lauridsen ◽

Karin Bjerre ◽

Michelle Geervliet Jensen ◽

Eric Johansen ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Animal Feed ◽

Bacterial Species ◽

Feed Additives ◽

Content Type ◽

Cutoff Values ◽

Antimicrobial Resistance Genes ◽

Species Specific

ABSTRACTBacillus megaterium(n= 29),Bacillus velezensis(n= 26),Bacillus amyloliquefaciens(n= 6),Bacillus paralicheniformis(n= 28), andBacillus licheniformis(n= 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C forB. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in oneB. megateriumstrain with an elevated chloramphenicol MIC compared to the otherB. megateriumstrains. InB. velezensisandB. amyloliquefaciens, a putative tetracycline efflux gene,tet(L), was found in all strains (n= 27) with reduced tetracycline susceptibility but was absent in susceptible strains. AllB. paralicheniformisand 23% ofB. licheniformisstrains had elevated MICs for erythromycin and harboredermD. The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCEWhen commercializing bacterial strains, likeBacillusspp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for fiveBacillusspecies were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

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Related Antimicrobial Resistance Genes Detected in Different Bacterial Species Co-isolated from Swine Fecal Samples

Foodborne Pathogens and Disease ◽

10.1089/fpd.2010.0695 ◽

2011 ◽

Vol 8 (6) ◽

pp. 663-679 ◽

Cited By ~ 19

Author(s):

Jonathan G. Frye ◽

Rebecca L. Lindsey ◽

Richard J. Meinersmann ◽

Mark E. Berrang ◽

Charlene R. Jackson ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Species ◽

Fecal Samples ◽

Antimicrobial Resistance Genes

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Benefits of Adding a Rapid PCR-Based Blood Culture Identification Panel to an Established Antimicrobial Stewardship Program

Journal of Clinical Microbiology ◽

10.1128/jcm.00996-16 ◽

2016 ◽

Vol 54 (10) ◽

pp. 2455-2463 ◽

Cited By ~ 55

Author(s):

Shawn H. MacVane ◽

Frederick S. Nolte

Keyword(s):

Antimicrobial Resistance ◽

Blood Culture ◽

Antimicrobial Stewardship ◽

Bacterial Species ◽

Effective Therapy ◽

Control Group ◽

Stewardship Program ◽

Antimicrobial Resistance Genes ◽

Culture Identification ◽

Organism Identification

Studies have demonstrated that the combination of antimicrobial stewardship programs (ASP) and rapid organism identification improves outcomes in bloodstream infections (BSI) but have not controlled for the incremental contribution of the individual components. Hospitalized adult patients with blood culture pathogens on a rapid, multiplex PCR-based blood culture identification panel (BCID) that included 19 bacterial species, 5Candidaspp., and 4 antimicrobial resistance genes were studied over sequential time periods in a pre-post quasiexperimental study in 3 groups in the following categories: conventional organism identification (controls), conventional organism identification with ASP (AS), and BCID with ASP (BCID). Clinical and economic outcomes were compared between groups. There were 783 patients with positive blood cultures; of those patients, 364 (115 control, 104 AS, and 145 BCID) met inclusion criteria. The time from blood culture collection to organism identification was shorter in the BCID group (17 h;P< 0.001) than in the control group (57 h) or the AS group (54 h). The BCID group had a shorter time to effective therapy (5 h;P< 0.001) than the control group (15 h) or AS group (13 h). The AS (57%) and BCID (52%) groups had higher rates of antimicrobial de-escalation than the control group (34%), with de-escalation occurring sooner in the BCID group (48 h;P= 0.034) than in the AS group (61 h) or the control group (63 h). No difference between the control group, AS group, and BCID group was seen with respect to mortality, 30-day readmission, intensive care unit length of stay (LOS), postculture LOS, or costs. In patients with BSI, ASP alone improved antimicrobial utilization. Addition of BCID to an established ASP shortened the time to effective therapy and further improved antimicrobial use compared to ASP alone, even in a setting of low antimicrobial resistance rates.

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Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Antibiotics ◽

10.3390/antibiotics10020221 ◽

2021 ◽

Vol 10 (2) ◽

pp. 221

Author(s):

Ashenafi F. Beyi ◽

Alan Hassall ◽

Gregory J. Phillips ◽

Paul J. Plummer

Keyword(s):

Antimicrobial Resistance ◽

Microbial Communities ◽

Resistance Genes ◽

Bacterial Species ◽

Tetracycline Resistance ◽

Digital Dermatitis ◽

Proximity Ligation ◽

Tetracycline Resistance Genes ◽

Complex Microbial Community ◽

Antimicrobial Resistance Genes

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

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Prevalence of pathogens harbouring mobile antimicrobial resistance genes and virulence factors in retail beef and mutton

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa089 ◽

2020 ◽

Vol 367 (12) ◽

Cited By ~ 1

Author(s):

Ying Liu ◽

Yifang Cui ◽

Wenjing Peng ◽

Baoyong Huang ◽

Lichao Ma ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Virulence Factors ◽

Bacterial Species ◽

Resistance Rate ◽

Human Beings ◽

Sensitivity Testing ◽

Whole Genome Analysis ◽

Extended Spectrum Beta Lactamase ◽

Antimicrobial Resistance Genes ◽

Different Sources

ABSTRACT Food safety is always a global issue, due to the increased dissemination of antimicrobial resistance and food poisoning related to foodborne bacterial pathogens. The purpose of this study was to assess the risk of potential foodborne bacteria of beef and mutton in retail stores. A total of 134 samples were collected from 24 local markets in Beijing, including raw and cooked beef or mutton, as well as samples derived from the corresponding environment and human beings. We obtained 674 isolates, of which Klebsiella spp. and Staphylococcus spp. were the dominant bacterial species in the meat samples and the environmental samples, respectively. Additionally, environmental bacteria are common in samples from different sources. Based on the results of antimicrobial sensitivity testing, resistance to tetracycline (with a resistance rate of 47.40%), amoxicillin + clavulanate (47.13%) and erythromycin (28.03%) were the major resistant phenotypes. According to the whole genome analysis, the extended spectrum beta-lactamase genes harboured by two K. pneumoniae strains isolated from cooked and raw beef were located on mobile elements. The major toxin genes of Bacillus cereus and adhesion- or invasion-related virulence factors were also shared among isolates from different sources. These factors pose potential risks to public health and need attention.

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HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

10.1101/2021.08.16.456459 ◽

2021 ◽

Author(s):

Lajos Kalmar ◽

Srishti Gupta ◽

Iain R. L. Kean ◽

Xiaoliang Ba ◽

Nazreen Hadjirin ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Gene ◽

Bacterial Species ◽

Antibiotic Use ◽

Antimicrobial Use ◽

Bioinformatics Pipeline ◽

Shotgun Metagenomics ◽

Antimicrobial Resistance Genes ◽

Conventional Farms ◽

Pig Farms

AbstractShotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli.Author SummaryAntimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.

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The Role of Gut Microbiota in Antimicrobial Resistance: A Mini-Review

Anti-Infective Agents ◽

10.2174/2211352517666190716154013 ◽

2020 ◽

Vol 18 (3) ◽

pp. 201-206

Author(s):

Farzaneh Firoozeh ◽

Mohammad Zibaei

Keyword(s):

Antimicrobial Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Bacterial Species ◽

Resistant Bacteria ◽

Human Gut ◽

Opportunistic Bacteria ◽

Antimicrobial Resistance Genes ◽

Opportunistic Pathogenic

In the current world, development and spread of antimicrobial resistance among bacteria have been raised and antimicrobial-resistant bacteria are one of the most important health challenges. The antimicrobial resistance genes can easily move and transfer among diverse bacterial species and strains. The human gut microbiota consists of a dense microbial population including trillions of microorganisms. Recently, studies have shown that the bacteria which make the major part of gut microbiota, harbor a variety of antimicrobial resistance genes which are called gut resistome. The transfer of resistance genes from commensal bacteria to gut-resident opportunistic bacteria may involve in the emergence of multi-drug resistant (MDR) bacteria. Thus, the main aim of the current mini-review was to study the mechanisms of exchange of antimicrobial resistance genes by commensal and opportunistic pathogenic bacteria in the human gut.

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Evolution of multi-resistance plasmids in Australian clinical isolates of Escherichia coli

Microbiology ◽

10.1099/mic.0.26773-0 ◽

2004 ◽

Vol 150 (5) ◽

pp. 1539-1546 ◽

Cited By ~ 31

Author(s):

Miranda Sherley ◽

David M. Gordon ◽

Peter J. Collignon

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Genetic Relationships ◽

Bacterial Species ◽

Host Cells ◽

Clinical Isolates ◽

Enzyme Electrophoresis ◽

Antimicrobial Resistance Genes ◽

Wide Range ◽

Resistance Plasmids

Plasmids allow the movement of genetic material, including antimicrobial resistance genes, between bacterial species and genera. They frequently mediate resistance to multiple antimicrobials and can result in the acquisition by a pathogen of resistance to all or most clinically relevant antimicrobials. Unfortunately, there are still large gaps in our understanding of how new multi-resistance plasmids evolve. Five Australian clinical institutions collaborated in this study of multi-resistance plasmids in clinical isolates of Escherichia coli. We characterized 72 resistance plasmids in terms of the antimicrobial resistance profile they conferred, their size and their incompatibility group. Restriction fragment length polymorphisms were used to determine the genetic relationships between the plasmids. Relationships between the host cells were determined using multi-locus enzyme electrophoresis. A lack of correlation between the evolutionary history of the host cells and their plasmids suggests that the horizontal transfer of resistance plasmids between strains of E. coli is common. The resistance plasmids were very diverse, with a wide range of resistance profiles and a lack of discrete evolutionary lineages. Multi-resistance plasmids did not evolve via the co-integrative capture of smaller resistance plasmids; rather, the roles of recombination and the horizontal movement of mobile genetic elements appeared to be most important.

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