Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family

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/.

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Investigation of the antibiotic resistance and biofilm formation of Staphylococcus aureus strains isolated from gangrenous mastitis of ewes

Acta Veterinaria Hungarica ◽

10.1556/avet.2012.016 ◽

2012 ◽

Vol 60 (2) ◽

pp. 189-197 ◽

Cited By ~ 7

Author(s):

Osman Tel ◽

Özkan Aslantaş ◽

Oktay Keskin ◽

Ebru Yilmaz ◽

Cemil Demir

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Virulence Factor ◽

Resistance Genes ◽

Biofilm Formation ◽

Antibiotic Resistance Genes ◽

Penicillin G ◽

Beta Lactamase ◽

Potential Virulence Factor ◽

Amoxicillin Clavulanic Acid

In this study,Staphylococcus aureusstrains (n = 110) isolated from seven ewe flocks in Sanliurfa, Turkey were screened for antibiotic resistance and biofilmforming ability as well as for genes associated with antibiotic resistance and biofilm-forming ability. All isolates were found to be susceptible to oxacillin, gentamicin, clindamycin, cefoxitin, tetracycline, vancomycin, amoxicillin-clavulanic acid, ciprofloxacin and sulphamethoxazole-trimethoprim. The percent proportions of strains resistant to penicillin G, ampicillin and erythromycin were 27.2% (n = 30), 25.4% (n = 28) and 6.3% (n = 7), respectively. Regarding the antibiotic resistance genes, 32 (29%) isolates carried theblaZ and 8 (7.2%) theermC gene. Other resistance genes were not detected in the isolates. All isolates showed biofilm-forming ability on Congo red agar (CRA), while 108 (98.18%) and 101 (91.81%) of them were identified as biofilm producers by the use of standard tube (ST) and microplate (MP) methods, respectively. All isolates carried theicaA andicaD genes but none of them harboured thebapgene. The results demonstrated thatS. aureusisolates from gangrenous mastitis were mainly resistant to penicillins (which are susceptible to the staphylococcal beta-lactamase enzyme), and less frequently to erythromycin. Furthermore, all of theS. aureusisolates produced biofilm which was considered a potential virulence factor in the pathogenesis of staphylococcal mastitis.

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An Orally Delivered Beta-Lactamase Protects the Gut Microbiome from Antibiotic-Mediated Damage and Mitigates the Propagation of Antibiotic-Resistance Genes in a Porcine Dysbiosis Model

Gastroenterology ◽

10.1016/s0016-5085(17)34350-0 ◽

2017 ◽

Vol 152 (5) ◽

pp. S1305-S1306

Author(s):

Sheila Connelly ◽

Christian Furlan Freguia ◽

Poorani Subramanian ◽

Nur A. Hasan ◽

Rita R. Colwell ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Beta Lactamase

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

Antibiotics ◽

10.3390/antibiotics10040419 ◽

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.

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Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage

Microorganisms ◽

10.3390/microorganisms7050150 ◽

2019 ◽

Vol 7 (5) ◽

pp. 150 ◽

Cited By ~ 4

Author(s):

Sheila Connelly ◽

Brian Fanelli ◽

Nur A. Hasan ◽

Rita R. Colwell ◽

Michael Kaleko

Keyword(s):

Antibiotic Resistance ◽

Small Intestine ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Oral Antibiotic ◽

Beta Lactamase ◽

Gi Tract ◽

Beta Lactam ◽

Beta Lactam Antibiotics

Antibiotics damage the gut microbiome, which can result in overgrowth of pathogenic microorganisms and emergence of antibiotic resistance. Inactivation of antibiotics in the small intestine represents a novel strategy to protect the colonic microbiota. SYN-004 (ribaxamase) is a beta-lactamase formulated for oral delivery intended to degrade intravenously administered beta-lactam antibiotics in the gastrointestinal (GI) tract. The enteric coating of ribaxamase protects the enzyme from stomach acid and mediates pH-dependent release in the upper small intestine, the site of antibiotic biliary excretion. Clinical benefit was established in animal and human studies in which ribaxamase was shown to degrade ceftriaxone in the GI tract, thereby preserving the gut microbiome, significantly reducing Clostridioides difficile disease, and attenuating antibiotic resistance. To expand ribaxamase utility to oral beta-lactams, delayed release formulations of ribaxamase, SYN-007, were engineered to allow enzyme release in the lower small intestine, distal to the site of oral antibiotic absorption. Based on in vitro dissolution profiles, three SYN-007 formulations were selected for evaluation in a canine model of antibiotic-mediated gut dysbiosis. Dogs received amoxicillin (40 mg/kg, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were measured after the first and last antibiotic doses and gut microbiomes were evaluated using whole genome shotgun sequence metagenomics analyses of fecal DNA prior to and after antibiotic treatment. Serum amoxicillin levels did not significantly differ +/- SYN-007 after the first dose for all SYN-007 formulations, while only one SYN-007 formulation did not significantly reduce systemic antibiotic concentrations after the last dose. Gut microbiomes of animals receiving amoxicillin alone displayed significant loss of diversity and emergence of antibiotic resistance genes. In contrast, for animals receiving amoxicillin + SYN-007, microbiome diversities were not altered significantly and the presence of antibiotic resistance genes was reduced. These data demonstrate that SYN-007 diminishes amoxicillin-mediated microbiome disruption and mitigates emergence and propagation of antibiotic resistance genes without interfering with antibiotic systemic absorption. Thus, SYN-007 has the potential to protect the gut microbiome by inactivation of beta-lactam antibiotics when administered by both oral and parenteral routes and to reduce emergence of antibiotic-resistant pathogens.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2020.519169 ◽

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.

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Resistome characterization of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolated from wastewater treatment utilities in Oregon

10.1101/2021.11.15.21266365 ◽

2021 ◽

Author(s):

Maeghan Easler ◽

Clint Cheney ◽

Jared D Johnson ◽

Marjan Khorshidi Zadeh ◽

Jacquelynn N Nguyen ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Wastewater Treatment ◽

Virulence Factors ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum

Infections resistant to broad spectrum antibiotics due to the emergence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae is of global concern. This study characterizes the resistome (i.e., entire ecology of resistance determinants) of 11 ESBL-producing Escherichia coli isolates collected from eight wastewater treatment utilities across Oregon. Whole genome sequencing was performed to identify the most abundant antibiotic resistance genes including ESBL-associated genes, virulence factors, as well as their sequence types. Moreover, the phenotypes of antibiotic resistance were characterized. ESBL-associated genes (i.e., blaCMY, blaCTX, blaSHV, blaTEM) were found in all but one of the isolates with five isolates carrying two of these genes (4 with blaCTX and blaTEM; 1 with blaCMY and blaTEM). The ampC gene and virulence factors were present in all the E. coli isolates. Across all the isolates, 31 different antibiotic resistance genes were identified. Additionally, all E. coli isolates harbored phenotypic resistance to beta-lactams (penicillins and cephalosporins), while eight of the 11 isolates carried multi-drug resistance phenotypes (resistance to three or more classes of antibiotics). Findings highlight the risks associated with the presence of ESBL-producing E. coli isolates in wastewater systems that have the potential to enter the environment and may pose direct or indirect risks to human health.

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Beta-lactamase and integron-associated antibiotic resistance genes of Klebsiella pneumoniae isolated from Tilapia fishes (Oreochromis niloticus)

Journal of Applied Pharmaceutical Science ◽

10.7324/japs.2019.90117 ◽

2019 ◽

Vol 9 (1) ◽

pp. 125-130

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Oreochromis Niloticus ◽

Antibiotic Resistance Genes ◽

Beta Lactamase

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Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome

10.1101/185348 ◽

2017 ◽

Cited By ~ 1

Author(s):

Sumayah F. Rahman ◽

Matthew R. Olm ◽

Michael J. Morowitz ◽

Jillian F. Banfield

Keyword(s):

Machine Learning ◽

Antibiotic Resistance ◽

Relative Abundance ◽

Resistance Genes ◽

Gut Microbiome ◽

Statistical Tests ◽

Antibiotic Resistance Genes ◽

Major Facilitator Superfamily ◽

Antibiotic Administration ◽

Beta Lactamase

AbstractAntibiotic resistance in pathogens is extensively studied, yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leverage genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We find that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly,Clostridium difficilestrains harboring this gene are at higher abundance in formula-fed infants compared toC. difficilelacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have faster replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data into five principal components classified by boosted decision trees. Among the genes involved in predicting if an organism increased in relative abundance after treatment are those that encode for subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics and predict how organisms in the gut microbiome will respond to antibiotic administration.ImportanceThe process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows for unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical and industrial applications.

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