scholarly journals Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic

2021 ◽  
Vol 11 ◽  
Author(s):  
Víctor V. Calderón ◽  
Roberto Bonnelly ◽  
Camila Del Rosario ◽  
Albert Duarte ◽  
Rafael Baraúna ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Rural Areas ◽  
Clinical Importance ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Bacterial Isolates ◽  
Santo Domingo

Bacteria carrying antibiotic resistance genes (ARGs) are naturally prevalent in lotic ecosystems such as rivers. Their ability to spread in anthropogenic waters could lead to the emergence of multidrug-resistant bacteria of clinical importance. For this study, three regions of the Isabela river, an important urban river in the city of Santo Domingo, were evaluated for the presence of ARGs. The Isabela river is surrounded by communities that do not have access to proper sewage systems; furthermore, water from this river is consumed daily for many activities, including recreation and sanitation. To assess the state of antibiotic resistance dissemination in the Isabela river, nine samples were collected from these three bluedistinct sites in June 2019 and isolates obtained from these sites were selected based on resistance to beta-lactams. Physico-chemical and microbiological parameters were in accordance with the Dominican legislation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses of ribosomal protein composition revealed a total of 8 different genera. Most common genera were as follows: Acinetobacter (44.6%) and Escherichia (18%). Twenty clinically important bacterial isolates were identified from urban regions of the river; these belonged to genera Escherichia (n = 9), Acinetobacter (n = 8), Enterobacter (n = 2), and Klebsiella (n = 1). Clinically important multi-resistant isolates were not obtained from rural areas. Fifteen isolates were selected for genome sequencing and analysis. Most isolates were resistant to at least three different families of antibiotics. Among beta-lactamase genes encountered, we found the presence of blaTEM, blaOXA, blaSHV, and blaKPC through both deep sequencing and PCR amplification. Bacteria found from genus Klebsiella and Enterobacter demonstrated ample repertoire of antibiotic resistance genes, including resistance from a family of last resort antibiotics reserved for dire infections: carbapenems. Some of the alleles found were KPC-3, OXA-1, OXA-72, OXA-132, CTX-M-55, CTX-M-15, and TEM-1.

scholarly journals Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1897 ◽  
Author(s):  
Amarachukwu Obayiuwana ◽  
Abasiofiok M. Ibekwe
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Human Health Risk ◽  
Antibiotic Resistance Genes ◽  
Wide Distribution ◽  
Mitigation Measures ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Bacterial Isolates ◽  
Human Pathogens

The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs need to be understood in order to design mitigation measures to combat their dissemination. Using the PCR analysis of genomic DNA, the prevalence of 41 ARGs active against the commonly used six classes of antibiotics was evaluated in 60 bacterial isolates obtained from pharmaceutical wastewaters in Nigeria. The ARGs most frequently detected from the bacterial isolates in each of the antibiotic classes under study include catA1 (58.3%); sulI (31.7%); tet(E) (30%); aac(3)-IV (28.3%); ermC (20%); blaTEM, blaCTX-M, blaNDM-1 at 18.3% each; which encode for resistance to chloramphenicol, sulfonamides, tetracycline, aminoglycoside, macrolide-lincosamide-streptogramin and β-lactams and penicillins, respectively. Acinetobacter spp., accession number MH396735 expressed the highest number of ARGs of all the bacterial isolates, having at least one gene that encodes for resistance to all the classes of antibiotics in the study. This study highlights wide distribution of ARB and ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

scholarly journals Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 419
Author(s):  
Tiago Cabral Borelli ◽  
Gabriel Lencioni Lovate ◽  
Ana Flavia Tonelli Scaranello ◽  
Lucas Ferreira Ribeiro ◽  
Livia Zaramela ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Functional Genomics ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Multi Drug Resistance ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Bacterial Strains

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.

scholarly journals Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

2020 ◽  
Author(s):  
Tiago Cabral Borelli ◽  
Gabriel Lencioni Lovate ◽  
Ana Flavia Tonelli Scaranello ◽  
Lucas Ferreira Ribeiro ◽  
Livia Zaramela ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
South America ◽  
Functional Genomics ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Multi Drug Resistance ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Bacterial Strains

AbstractThe rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative and Gram-positive bacteria, including the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. We identify a high abundance of beta-lactamase genes in highly resistant organisms, including seven extended-spectrum β-lactamases shared between organisms from different species. Additionally, we identify several ARGs-carrying plasmids indicating the potential for fast transmission of resistance mechanism between bacterial strains, comprising a novel IncFII plasmid recently introduced in Brazil from Asia. Through comparative genomic analysis, we demonstrate that some pathogens identified here are very distantly related to other bacteria isolated worldwide, demonstrating the potential existence of endemic bacterial pathogens in Brazil. Also, we uncovered at least two couples of (near)-identical plasmids exhibiting multi-drug resistance, suggesting that plasmids were transmitted between bacteria of the same or different species in the hospital studied. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identify six beta-lactamase genes out of 15 predicted in silico as the main responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms.ImportanceBig data and large-scale sequencing projects have revolutionized the field, achieving a greater understanding of ARGs identification and spreading at global level. However, given that microbiota and associated ARGs may fluctuate across geographic zones, hospital-associated infections within clinical units still remain underexplored in Brazil – the largest country in South America; 210 million inhabitants – and neighboring countries. This work highlighted the identification of several ARGs shared between species co-occurring simultaneously into a Brazilian hospital, some of them associated with large plasmids, mostly endowed with transposable elements. Also, genomic features of clinically underrepresented pathogens such M. morganii and B. cepacia were revealed. Taken together, our results demonstrate how structural and functional genomics can help to identify emerging mechanisms of shared antibiotic resistance in bacteria from clinical environments. Systematic studies as the one presented here should help to prevent outbreaks of novel multidrug resistance bacteria in healthcare facilities.

Quintuplex PCR to Detect Antibiotic Resistance Genes in Streptococcus pneumoniae

2016 ◽  
Vol 1 (2) ◽  
pp. 22 ◽  
Author(s):  
Navindra Kumari Palanisamy ◽  
Parasakthi Navaratnam ◽  
Shamala Devi Sekaran
Keyword(s):  
Antibiotic Resistance ◽  
Streptococcus Pneumoniae ◽  
Resistance Genes ◽  
Bacterial Pathogen ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Penicillin Resistance ◽  
Penicillin Binding Proteins ◽  
Efflux Mechanism ◽  
Mic Value

Introduction: Streptococcus pneumoniae is an important bacterial pathogen, causing respiratory infection. Penicillin resistance in S. pneumoniae is associated with alterations in the penicillin binding proteins, while resistance to macrolides is conferred either by the modification of the ribosomal target site or efflux mechanism. This study aimed to characterize S. pneumoniae and its antibiotic resistance genes using 2 sets of multiplex PCRs. Methods: A quintuplex and triplex PCR was used to characterize the pbp1A, ermB, gyrA, ply, and the mefE genes. Fifty-eight penicillin sensitive strains (PSSP), 36 penicillin intermediate strains (PISP) and 26 penicillin resistance strains (PRSP) were used. Results: Alteration in pbp1A was only observed in PISP and PRSP strains, while PCR amplification of the ermB or mefE was observed only in strains with reduced susceptibility to erythromycin. The assay was found to be sensitive as simulated blood cultures showed the lowest level of detection to be 10cfu. Conclusions: As predicted, the assay was able to differentiate penicillin susceptible from the non-susceptible strains based on the detection of the pbp1A gene, which correlated with the MIC value of the strains.

scholarly journals HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yu Li ◽  
Zeling Xu ◽  
Wenkai Han ◽  
Huiluo Cao ◽  
Ramzan Umarov ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Deep Learning ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Third Party ◽  
Superior Performance ◽  
Beta Lactamase ◽  
Learning Framework ◽  
Sequence Encoding ◽  
Global Threat

Abstract Background The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs. Results Here, we propose an end-to-end Hierarchical Multi-task Deep learning framework for ARG annotation (HMD-ARG). Taking raw sequence encoding as input, HMD-ARG can identify, without querying against existing sequence databases, multiple ARG properties simultaneously, including if the input protein sequence is an ARG, and if so, what antibiotic family it is resistant to, what resistant mechanism the ARG takes, and if the ARG is an intrinsic one or acquired one. In addition, if the predicted antibiotic family is beta-lactamase, HMD-ARG further predicts the subclass of beta-lactamase that the ARG is resistant to. Comprehensive experiments, including cross-fold validation, third-party dataset validation in human gut microbiota, wet-experimental functional validation, and structural investigation of predicted conserved sites, demonstrate not only the superior performance of our method over the state-of-art methods, but also the effectiveness and robustness of the proposed method. Conclusions We propose a hierarchical multi-task method, HMD-ARG, which is based on deep learning and can provide detailed annotations of ARGs from three important aspects: resistant antibiotic class, resistant mechanism, and gene mobility. We believe that HMD-ARG can serve as a powerful tool to identify antibiotic resistance genes and, therefore mitigate their global threat. Our method and the constructed database are available at http://www.cbrc.kaust.edu.sa/HMDARG/.

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 Prevalence And Characterization Of Plasmid-Mediated Quinolone Resistance In Various Aquatic Sources

2021 ◽  
Author(s):  
Farhan Yusuf ◽  
Kimberley Gilbride
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Quinolone Resistance ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Environmental Isolates ◽  
Topoisomerase Iv ◽  
Phenotypic Resistance ◽  
Ciprofloxacin Resistance

Bacterial isolates found in aquatic ecosystems often carry antibiotic resistance genes (ARGs). These ARGs are often found on plasmids and transposons, which allows them to be proliferate throughout bacterial communities via horizontal gene transfer (HGT) causing dissemination of multidrug resistance. The increase in antibiotic resistance has raised concerns about the ability to continue to use these drugs to fight infectious diseases. Novel synthetic antibiotics like ciprofloxacin that are not naturally found in the environment were developed to prevent resistances. However, ciprofloxacin resistance has occurred through chromosomal gene mutations of type 2 topoisomerases or by the acquisition of plasmid-mediated quinolone resistances (PMQR). A particular PMQR, qnr genes, encoding for pentapeptide repeat proteins that confer low levels of quinolone resistance and protect DNA gyrase and topoisomerase IV from antibacterial activity. These qnr genes have been identified globally in both clinical and environmental isolates. The aim of this study was to determine the prevalence of ciprofloxacin-resistant bacteria in aquatic environments in the Greater Toronto Area and the potential dissemination of ciprofloxacin resistance. With the selective pressure of ciprofloxacin, we hypothesize that ciprofloxacin-resistant bacteria (CipR) in the environment may carry PMQR mechanisms while the sensitive population (CipS) would not carry PMQR genes. Isolates were tested for resistance to an additional 12 different antibiotics and identified using Sanger sequencing PCR products of the 16S rRNA gene. To determine which genes are responsible for ciprofloxacin resistance, multiplex PCR of associated qnr genes, qnrA, qnrB, and qnrS, was carried out on 202 environmental isolates. Our data demonstrate a similar prevalence of qnr genes was found in CipR (19%) and CipS (14%) populations suggesting that the presence of these genes was not necessarily correlated with the phenotypic resistance to the antibiotic. Furthermore, ciprofloxacinresistant bacteria were found in all locations at similar frequencies suggesting that resistance genes are widespread and could possibly arise through HGT events. Overall, determining the underlying cause and prevalence of ciprofloxacin resistance could help re-establish the effectiveness of these antimicrobial compounds.

scholarly journals Antibiotic resistance in lactococci and enterococci: phenotypic and molecular-genetic aspects

2017 ◽  
Vol 1 (1) ◽  
pp. 10-17
Author(s):  
Danuta Plotnikava ◽  
Anastasiya Sidarenka ◽  
Galina Novik
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Antibiotic Resistance Genes ◽  
Public Health Problem ◽  
Animal Husbandry ◽  
Resistant Bacteria ◽  
Monitoring And Control ◽  
Bacterial Drug Resistance

Abstract Extensive use of antibiotics in medicine, veterinary practice and animal husbandry has promoted the development and dissemination of bacterial drug resistance. The number of resistant pathogens causing common infectious diseases increases rapidly and creates worldwide public health problem. Commensal bacteria, including lactic acid bacteria of genera Enterococcus and Lactococcus colonizing gastrointestinal and urogenital tracts of humans and animals may act as vehicles of antibiotic resistance genes similar to those found in pathogens. Lactococci and enterococci are widely used in manufacturing of fermented products and as probiotics, therefore monitoring and control of transmissible antibiotic resistance determinants in industrial strains of these microorganisms is necessary to approve their Qualified Presumption of Safety status. Understanding the nature and molecular mechanisms of antibiotic resistance in enterococci and lactococci is essential, as intrinsic resistant bacteria pose no threat to environment and human health in contrast to bacteria with resistance acquired through horizontal transfer of resistance genes. The review summarizes current knowledge concerning intrinsic and acquired antibiotic resistance in Lactococcus and Enterococcus genera, and discusses role of enterococci and lactococci in distribution of this feature.

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