scholarly journals Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

2019 ◽  
Author(s):  
Kern Rei Chng ◽  
Chenhao Li ◽  
Denis Bertrand ◽  
Amanda Hui Qi Ng ◽  
Junmei Samantha Kwah ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Ecological Niches ◽  
Metagenomic Sequencing ◽  
Resistant Strains

AbstractThere is growing attention surrounding hospital acquired infections (HAIs) due to high associated healthcare costs, compounded by the scourge of widespread multi-antibiotic resistance. Although hospital environment disinfection is well acknowledged to be key for infection control, an understanding of colonization patterns and resistome profiles of environment-dwelling microbes is currently lacking. We report the first extensive genomic characterization of microbiomes (428), common HAI-associated microbes (891) and transmissible drug resistance cassettes (1435) in a tertiary hospital environment based on a 3-timepoint sampling (1 week and >1 year apart) of 179 sites from 45 beds. Deep shotgun metagenomic sequencing unveiled two distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human microbiome influenced environments that display corresponding patterns of divergence over space and time. To study common nosocomial pathogens that were typically present at low abundances, a combination of culture enrichment and long-read nanopore sequencing was used to obtain thousands of high contiguity genomes (2347), phage sequences (1693) and closed plasmids (5910), a significant fraction of which (>60%) are not represented in current sequence databases. These high-quality assemblies and metadata enabled a rich characterization of resistance gene combinations, phage diversity, plasmid architectures, and the dynamic nature of hospital environment resistomes and their reservoirs. Phylogenetic analysis identified multidrug resistant strains as being more widely distributed and stably colonizing across hospital sites. Further genomic comparisons with clinical isolates across multiple species supports the hypothesis that multidrug resistant strains can persist in the hospital environment for extended periods (>8 years) to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in the hospital environment and establishes the feasibility of systematic genomic surveys to help target resources more efficiently for preventing HAIs.

scholarly journals Comprehensive Genome Analysis of Carbapenem-Resistant Strains of Raoultella Species, an Emerging Multidrug-Resistant Bacterium in Hospitals

2019 ◽  
Vol 63 (12) ◽  
Author(s):  
Xiao Yu ◽  
Beiwen Zheng ◽  
Jing Zhang ◽  
Hao Xu ◽  
Tingting Xiao ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Control Measures ◽  
Carbapenem Resistant ◽  
Multidrug Resistant Bacterium ◽  
The World ◽  
Resistant Strains

ABSTRACT We report the characterization of six carbapenem-resistant Raoultella spp. (CRRS) in our hospital and a genomic analysis of 58 publicly available isolates. CRRS isolates are sporadically identified around the world, and different transposons carrying carbapenemases were the resistant mechanisms. Mobile genetic elements play an important role in acquiring antibiotic resistance genes from the hospital. An improved understanding of these transposon and targeted control measures will be very valuable to prevent CRRS dissemination.

scholarly journals Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

2020 ◽  
Vol 26 (6) ◽  
pp. 941-951 ◽  
Author(s):  
Kern Rei Chng ◽  
◽  
Chenhao Li ◽  
Denis Bertrand ◽  
Amanda Hui Qi Ng ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Tertiary Hospital ◽  
Hospital Environment ◽  
Opportunistic Pathogens

scholarly journals Characterization of Tn7-like transposons and its related antibiotic resistance among Enterobacteriaceae from livestock and poultry in China

2020 ◽  
Author(s):  
Juan He ◽  
Cui Li ◽  
Pengfei Cui ◽  
Hongning Wang
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Horizontal Transmission ◽  
Antibiotic Resistance Genes ◽  
Variable Region ◽  
Multidrug Resistant ◽  
Antibiotic Resistant ◽  
E Coli ◽  
New Type

Abstract Background: This study was aimed to investigate the prevalence and structure of Tn7-like in Enterobacteriaceae from livestock and poultry as well as their possible role as reservoir of antibiotic resistance genes (ARGs).Methods: Polymerase chain reaction (PCR) and DNA sequencing analyses were used for the characterization of Tn7-like, associated integrons and ARGs. The antimicrobial resistance profile of the isolates was examined by using disc diffusion test.Results: Three hundred and seventy-eight Tn7-like-positive strains of Enterobacteriaceae were isolated, and included E. coli (128), Proteus(150), K. pneumonia(17), Salmonella(13), M. morganii (21) and A. baumannii(1), wherein high resistance was observed for Trimethoprim/Sulfamethoxazole and Streptomycin, and fifty percent of the strains were multidrug-resistant. Integrons class 2 were detected in all of the isolates and there are high frequency mutation sites especially in 535, a stop mutation. Variable region of class 2 integrons carried same gene cassettes, namely aadA1-sat2-dfrA1. From the 378 isolated strains, we found a new type of Tn7-like on a plasmid, named Tn6765.Conclusions: These findings proved that the Tn7-like can contribute to the horizontal transmission of antibiotic resistant genes in livestock and poultry. As potential vessels for antibiotic resistance genes (ARGs), Tn7-like could not be ignored due to their efficient transfer ability in environments.

scholarly journals Phenotypic and genotypic evaluation of antibiotic resistance and molecular characterization of Streptococcus species isolated from hospital cockroaches

2020 ◽  
Author(s):  
Mohammad Chehelgerdi ◽  
Reza Ranjbar
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Bacterial Culture ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Hospital Environment ◽  
Streptococcus Species ◽  
Antibiotic Resistance Properties

Abstract Background The present investigation aimed to assess the antibiotic resistance properties and distribution of virulence factors in the Streptococcus spp. isolated from hospital cockroaches. Methods Six-hundred and sixty cockroach samples were collected. Cockroaches were vigorously washed with normal saline, and the achieved saline was used for bacterial culture. Isolated Streptococcus spp. were subjected to disk diffusion as well as PCR amplification of virulence factors and antibiotic resistance genes. Results Prevalence of S. pyogenes, S. agalactiae and S. pneumonia was 4.82%, 1.66% and 6.96%, respectively. The highest prevalence of S. pyogenes, S. agalactiae and S. pneumonia were found in oriental (5.71%), oriental (2.85%) and American (7.71%) cockroaches, respectively. Cfb (53.93%), cyl (52.8%), scaa (51.68%) and glna (50.56%) were the most commonly detected streptococcal virulence factors. Pbp2b (71.91%), pbp2 × (58.42%), mefA (46.06%), ermB (46.06%) and tetM (46.06%) were the most commonly detected antibiotic resistance genes. Streptococcal spp. exhibited the highest prevalence of resistance against tetracycline (80.89%), trimethoprim (65.16%), and penicillin (56.17%). Conclusion To the best of our knowledge, this is the first prevalence report of virulence factors and antibiotic resistance genes in the Streptococcal spp. isolated from American, German and oriental hospital cockroaches. Findings recommended a certain role for cockroaches in the transmission of nosocomial infections and particularly those caused by virulent and resistant Streptococcus spp. in the hospital environment.

scholarly journals Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Noha Ahmed Abd Alfadil ◽  
Malik Suliman Mohamed ◽  
Manal M. Ali ◽  
El Amin Ibrahim El Nima
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Contamination Level ◽  
Rdna Sequencing ◽  
Resistant Strains

Background. Banknotes are one of the most exchangeable items in communities and always subject to contamination by pathogenic bacteria and hence could serve as vehicle for transmission of infectious diseases. This study was conducted to assess the prevalence of contamination by pathogenic bacteria in Sudanese banknotes, determine the susceptibility of the isolated organisms towards commonly used antibiotics, and detect some antibiotic resistance genes.Methods. This study was carried out using 135 samples of Sudanese banknotes of five different denominations (2, 5, 10, 20, and 50 Sudanese pounds), which were collected randomly from hospitals, food sellers, and transporters in all three districts of Khartoum, Bahri, and Omdurman. Bacterial prevalence was determined using culture-based techniques, and their sensitivity patterns were determined using the Kirby–Bauer disk diffusion method. Genotypic identification was carried out using PCR and 16S rDNA sequencing. Antibiotic resistance genes of some isolates were detected using PCR technique.Results. All Sudanese banknotes were found to be contaminated with pathogenic bacteria.Klebsiella pneumoniaewas found to be the most frequent isolate (23%), whereasBacillus mycoides(15%) was the most abundant Gram-positive isolate. There was a significant relationship between the number of isolates and the banknote denomination withpvalue <0.05 (the lower denomination showed higher contamination level). Our study has isolated bacteria that are resistant to penicillins and cephalosporins. Multidrug-resistant strains harboring resistant genes (mecA,blaCTX-M, andblaTEM) were also detected.Conclusion. All studied Sudanese banknotes were contaminated with pathogenic bacteria, including multidrug-resistant strains, and may play a significant role in the transmission of bacterial infections.

scholarly journals Multidrug-resistant enterococci in the hospital environment: detection of novel vancomycin-resistant E. faecium clone ST910

2016 ◽  
Vol 10 (08) ◽  
pp. 799-806 ◽  
Author(s):  
Raoudha Dziri ◽  
Carmen Lozano ◽  
Leila Ben Said ◽  
Ridha Bellaaj ◽  
Abdellatif Boudabous ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Positive Sample ◽  
Hospital Environment ◽  
Resistant Bacteria ◽  
Antimicrobial Resistance Genes ◽  
Vancomycin Resistant

Introduction: The role of the hospital environment as a reservoir of resistant bacteria in Tunisia has been poorly investigated; however, it could be responsible for the transmission of multidrug-resistant bacteria. The objective was to study the prevalence of Enterococcus in the environment of a Tunisian hospital and the antibiotic resistance phenotype/genotype in recovered isolates, with special reference to vancomycin resistance. Methodology: A total of 300 samples were taken (March–June, 2013) and inoculated in Slanetz-Bartley agar plates supplemented or not supplemented with 8 µg/mL of vancomycin. Antibiotic resistance genes were tested by polymerase chain reaction (PCR). The clonal relatedness of the vanA isolates was assessed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence testing (MLST). Results: Enterococci were recovered in 33.3% of tested samples inoculated in SB medium. E faecium was the most prevalent species, followed by E. faecalis and E. casseliflavus. Antimicrobial resistance genes detected were as follows (number of isolates): erm(B) (71), tet(M) (18), aph(3’)-IIIa (27), ant(6)-Ia (15), cat(A) (4), and van(C2) (6). Vancomycin-resistant-enterococci (VRE) were recovered from 14 samples (4.7%), when tested in SB-VAN. The 14 VRE (one per positive sample) were identified as E. faecium and contained the van(A),erm(B), tet(M), ant(6)-Ia, and aph(3’)-IIIa genes. Thirteen of the VRE strains were ascribed by PFGE and MLST to a novel clone (new ST910), and only one VRE strain was typed as ST80 included in CC17. Conclusions: The emergence and spread of new clones of VRE, especially in the hospital environment in this country, could become particularly problematic.

scholarly journals Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ishi Keenum ◽  
Robert K. Williams ◽  
Partha Ray ◽  
Emily D. Garner ◽  
Katharine F. Knowlton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Land Application ◽  
Multidimensional Analysis ◽  
Small Scale ◽  
Antibiotic Administration ◽  
Metagenomic Sequencing ◽  
Combined Effects ◽  
Bacterial Microbiota

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

scholarly journals Environmental Spread of New Delhi Metallo-β-Lactamase-1-Producing Multidrug-Resistant Bacteria in Dhaka, Bangladesh

2017 ◽  
Vol 83 (15) ◽  
Author(s):  
Mohammad Aminul Islam ◽  
Moydul Islam ◽  
Rashedul Hasan ◽  
M. Iqbal Hossain ◽  
Ashikun Nabi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Tap Water ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
New Delhi ◽  
Multidrug Resistant Bacteria ◽  
Content Type ◽  
Wastewater Samples

ABSTRACT Resistance to carbapenem antibiotics through the production of New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor the possible source of the spread of these organisms in Dhaka, Bangladesh, we conducted a comparative analysis of wastewater samples from hospital-adjacent areas (HAR) and from community areas (COM), as well as public tap water samples, for the occurrence and characteristics of NDM-1-producing bacteria. Of 72 HAR samples tested, 51 (71%) samples were positive for NDM-1-producing bacteria, as evidenced by phenotypic tests and the presence of the bla NDM-1 gene, compared to 5 of 41 (12.1%) samples from COM samples (P < 0.001). All tap water samples were negative for NDM-1-producing bacteria. Klebsiella pneumoniae (44%) was the predominant bacterial species among bla NDM-1-positive isolates, followed by Escherichia coli (29%), Acinetobacter spp. (15%), and Enterobacter spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes, including bla CTX-M-1 (80%), bla CTX-M-15 (63%), bla TEM (76%), bla SHV (33%), bla CMY-2 (16%), bla OXA-48-like (2%), bla OXA-1 (53%), and bla OXA-47-like (60%) genes. Around 40% of the isolates contained a qnr gene, while 50% had 16S rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30 to 50 MDa carrying bla NDM-1 were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multidrug-resistant bacteria as a potential public health threat. In view of the existing practice of discharging untreated liquid waste into the environment, hospitals in Dhaka city contribute to the potential dissemination of NDM-1-producing bacteria into the community. IMPORTANCE Infections caused by carbapenemase-producing Enterobacteriaceae are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently described carbapenemase, and the bla NDM-1 gene, which encodes NDM-1, is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows a high prevalence of NDM-1-producing organisms in the wastewater samples from hospital-adjacent areas as a potential source for the spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines the characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple-antibiotic-resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.

scholarly journals CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

mSphere ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Valerie J. Price ◽  
Wenwen Huo ◽  
Ardalan Sharifi ◽  
Kelli L. Palmer
Keyword(s):  
Antibiotic Resistance ◽  
High Risk ◽  
Enterococcus Faecalis ◽  
Resistance Genes ◽  
Treatment Options ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Content Type ◽  
New Genes ◽  
Restriction Modification

ABSTRACT Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics. Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.

Sign in / Sign up

Export Citation Format

Share Document