Spread Of Resistance Genes Research Articles

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner

Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-naïve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.

Susceptibility of Anopheles gambiae sensu lato to different insecticide classes and mechanisms involved in the South-North transect of Benin

Monitoring vector resistance to insecticides is a major component of resistance management. Adults of Anopheles gambiae s.l. from larvae collected at thirteen sites were tested with papers impregnated with bendiocarb, permethrin; deltamethrin; pirimiphos-methyl and induced bottles of insecticide including bendiocarb; deltamethrin, permethrin and pirimiphos-methyl. Molecular analyses were performed and detoxification enzyme levels were determined for each study site. This study revealed a generalized distribution of resistance of An. gambiae s.l. to pyrethroids (permethrin and deltamethrin) and a clear resistance to carbamates (bendiocarb) especially in the northern region of the country. This vector is still susceptible to organophosphates, especially pirimiphos-methyl, but resistance is a dynamic phenomenon and it would be necessary to monitor the susceptibility of these anopheles to pyrimiphos-methyl and to find alternative vector control methods to slow down the spread of resistance genes.

Synergism between Rifampicin and Cationic Polyurethanes Overcomes Intrinsic Resistance of Escherichia coli

Antibiotic-resistant Gram-negative bacteria are emergent pathogens, causing millions of infections worldwide. While there are several classes of antibiotics that are effective against Gram-positive bacteria, the outer membrane (OM) of Gram-negative bacteria excludes high-molecular-weight hydrophobic antibiotics, making these species intrinsically resistant to several classes of antibiotics, including polyketides, aminocoumarins, and macrolides. The overuse of antibiotics such as β-lactams has also promoted the spread of resistance genes throughout Gram-negative bacteria, including the production of extended spectrum β-lactamases (ESBLs). The combination of innate and acquired resistance makes it extremely challenging to identify antibiotics that are effective against Gram-negative bacteria. In this study, we have demonstrated the synergistic effect of outer membrane-permeable cationic polyurethanes with rifampicin, a polyketide that would otherwise be excluded by the OM, on different strains of E. coli, including a clinically isolated uropathogenic multidrug-resistant (MDR) E. coli. Rifampicin combined with a low-dose treatment of a cationic polyurethane reduced the MIC in E. coli of rifampicin by up to 64-fold. The compositions of cationic polyurethanes were designed to have low hemolysis and low cell cytotoxicity while maintaining high antibacterial activity. Our results demonstrate the potential to rescue the large number of available OM-excluded antibiotics to target normally resistant Gram-negative bacteria via synergistic action with these cationic polyurethanes, acting as a novel antibiotic adjuvant class.

Effects of Sulfamethoxazole on Growth and Antibiotic Resistance of A Natural Microbial Community

Diffuse environmental antibiotic and antibiotic resistance gene contamination is increasing human and animal exposure to these emerging compounds with a consequent risk of reduction in antibiotic effectiveness. The present work investigated the effect of the antibiotic sulfamethoxazole (SMX) on growth and antibiotic resistance genes of a microbial community collected from an anaerobic digestion plant fed with cattle manure. Digestate samples were used as inoculum for concentration-dependent experiments using SMX at various concentrations. The antibiotic concentrations affecting the mixed microbial community in terms of growth and spread of resistant genes (sul1, sul2) were investigated through OD (Optical Density) measures and qPCR assays. Moreover, SMX biodegradation was assessed by LC-MS/MS analysis. The overall results showed that SMX concentrations in the range of those found in the environment did not affect the microbial community growth and did not select for antibiotic-resistant gene (ARG) maintenance or spread. Furthermore, the microorganisms tested were able to degrade SMX in only 24 h. This study confirms the complexity of antibiotic resistance spread in real matrices where different microorganisms coexist and suggests that antibiotic biodegradation needs to be included for fully understanding the resistance phenomena among bacteria.

Characteristics of bacterial community and ARGs profile in engineered goldfish tanks with stresses of sulfanilamide and copper

Abuse of antibiotics in aquaculture have been alarming and might aggravate spread of resistance genes in the environment. Holistic ARGs proliferation checks require deeper analyses of coupled absolute abundances in 16S rRNA bacteria communities at the phylum level to detect biomarkers. Sulfanilamide (sul) and copper II sulfate (CuSO4 II) were, therefore, designed and added asseparate or combined treatments in 9 replicate engineered goldfish tanks comprising 3 individual sul, 3 CuSO4 II, 3 (sul + CuSO4 II) combinations, and 3 controls within 180days. The DNA from water and fish guts was sequenced under qPCR to determine 16S rRNA bacteria biomarkers co-occurring with the correspondent ARGs. Combined chemical addition at 0.8-1.5mg sul + 0.5-1.0mg CuSO4 II/3L of tank waters reduced sequenced 16S rRNA bacteria absolute abundances in fish gut and water samples while portraying the biomarkers. Absolute abundances of the entire 16S rRNA bacteria was higher in fish guts (3.4 × 1014-4.9 × 108 copies/g) than water samples (1.5 × 109-2.6 × 1015 copies/L), respectively. Much as sul 1(log) were dominant over intl 1(log) genes, and their fundamental profiles were also higher in the fish guts than water samples; the Spearman's correlation analyses revealed positive relationship (p< 0.01 and r= 0.873) among the biomarkers of both ARG pairs at the phylum level and the physicochemical parameters. In the fish gut and water samples ratios, Bacteroidetes (10-85:12-85%)> Proteobacteria (10-50:15-65%) >Planktomycetes (10-52:8-25%) featured prominently based on LEfSe use as the hot-spotted biomarkers, hence justifying its higher prospects towards innovative environmental microbiological and biotechnological studies.

First detection of mobilized colistin resistance mcr-1 gene in Escherichia coli isolated from livestock and sewage in Iran

Currently, few studies have investigated the mechanisms of resistance to colistin in Iran. The aim of this study was to investigate mcr-harbouring Escherichia coli dissemination in livestock and sewage in Iran. A total of 115 samples from cows (n = 38), chickens (n = 47) and urban sewage samples (n = 30) were collected. The presence of genes including mcr1–6 and ampC β-lactamase (blaMOX, blaCIT, blaDHA, blaACC, blaEBC, blaFOX) for colistin-resistant isolates was investigated by multiplex PCR method. Genetic association of colistin-resistant strains was also evaluated by ERIC PCR. Sixty-five isolates were identified as E. coli. Meaningless were resistant to colistin. The highest (26.1%) and lowest (3.07%) resistance were shown to ampicillin and meropenem respectively. Among the three colistin-resistant isolates, 2 (66%) were multidrug resistant, with one of them being mcr-1 positive and the other one positive for DHA ampC β-lactamase gene. No mcr2–6 genes were found. Minimum inhibitory concentration of mcr-producing isolate was 4 mg/L by microbroth dilution. This study reports, first the detection of mcr-1 in E. coli from farm animals in Iran, a finding that is indicative of a global distribution of this plasmidic element and threatning the use of colistin as a last resort antibiotic. No clonal relationship was observed between the colistin-resistant E. coli isolates by ERIC-PCR. Monitoring the presence of these strains in animal sources help as to controlling the spread of resistance genes from animal to human is vital.

Occurrence, effects and behaviour of the antibiotic lincomycin in the agricultural and aquatic environment - A review.

Lincomycin, an antibiotic commonly used in veterinary medicine, is frequently detected within the agricultural environment. The active compound enters the aquatic environment after manure application via infiltration or surface run-off, where it may negatively affect non-target organisms and contribute to the development and spread of resistant genes. However, a review on the fate of lincomycin within the agricultural and aquatic environment is lacking. Hence, to provide an overview, the main part of this paper summarizes the current literature on the occurrence, effects and behaviour of lincomycin in all relevant environmental compartments, including manure, soil, surface water and groundwater. Lincomycin was regularly detected in all environmental compartments and even in the food chain, appeared to sorb temporarily and mainly in its cationic microspecies, and dissipated after time periods that could cover days, months, or years, depending on the compartment and conditions. As noticed during the literature research conducted, information on the attenuation of lincomycin in terms of biological degradation in the aquatic environment is widely lacking, although it seems that biodegradation is the major removal mechanism. Therefore, a laboratory study, implemented by means of batch experiments, was carried out in order to evaluate the biological degradation of lincomycin in the aquatic environment. First order degradation started after a start-up phase of 10-14days with a degradation rate constant of 0.55 d-1 and a half-life time of 30h. Further, the degradation rate constant was found to be independent of initial concentrations as long as concentrations did not exceed a concentration level at which the bacteria were inhibited, as it was the case in this study at a concentration of 10mgL-1. Biodegradation was confirmed as an important degradation pathway for LIN in the aquatic environment.

Fate of antibiotic resistance genes and metal resistance genes during the thermophilic fermentation of solid and liquid swine manures in an ectopic fermentation system

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44–97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

Integron and its role in antimicrobial resistance: A literature review on some bacterial pathogens.

In recent years, different acquired resistance mechanisms, including transposons, bacteriophages, plasmids, and integrons have been identified as involved in the spread of resistance genes in bacteria. The role of integrons as mobile genetic elements playing a central role in antibiotic resistance has been well studied and documented. Integrons are the ancient structures that mediate the evolution of bacteria by acquiring, storing, disposing, and resorting to the reading frameworks in gene cassettes. The term integron describes a large family of genetic elements, all of which are able to capture gene cassettes. Integrons were classified into three important classes based on integrase intI gene sequence. Integrons can carry and spread the antibiotic resistance genes among bacteria and are among the most significant routes of distribution of resistance genes via horizontal transfer. All integrons have three essential core features. The first feature is intI, the second one is an integron-associated recombination site, attI, and an integron-associated promoter, Pc, is the last feature. Among them, the class 1 integron is a major player in the dissemination of antibiotic resistance genes across pathogens and commensals. Various classes of integrons possessing a wide variety of gene cassettes are distributed in bacteria throughout the world. This review thus focuses on the distribution of integrons among important bacteria.

Characterization of blaCMY-2-carrying IncC and rmtB-carrying IncI1/ST136 plasmids in an avian Escherichia coli ST224 strain

To analyze characteristics and underlying evolutionary processes of IncC and IncI1 plasmids in a multidrug-resistant avian E. coli strain, antibiotic susceptibility testing, PCR, conjugation assays, and next-generation sequencing were performed. The type 1 IncC plasmid pEC009.1 harbored three antimicrobial resistance regions including ISEcp1-blaCMY-2-blc-sugE, ARI-B resistance island, and ARI-A island that was a mosaic multidrug resistance region (MRR) comprised of a class 1 integron with cassette array |aac(6′)-II(aacA7)|qacE∆1|sul1|, IS26-mphR(A)-mrx-mph(A)-IS26, IS26-fosA3-IS26, and mercury resistance cluster merRTPABDE. It is the first report of three different size circular forms derived from IS26-mphR(A)-mrx-mph(A)-IS26-fosA3-IS26 in ARI-A of type 1 IncC plasmid. In IncI1/ST136 pEC009.2, the truncated transposon Tn1722 carrying blaTEM-1b, rmtB, aac(3)-IId(aacC2d), and a class 1 integron with cassette array |dfrA12|orfF|aadA2|, inserted into the plasmid backbone generating 5-bp direct repeats (DRs, TATAA) at the boundaries of the region, which was highly similar to that of other IncI1 plasmids, and differed by the arrangements of resistance determinants. Comparison among two epidemic plasmid lineages showed complex MRRs respectively located in the specific position in type 1 IncC and IncI1/ST136 plasmids with conserved backbones, and these have evolved via multiple events involved in mobile elements-mediated loss and gain of resistance genes and accessory genes. Strains harboring these plasmids may serve as a reservoir for antibiotic resistance genes, thereby contributing to the rapid spread of resistance genes and posing a public health threat.

Understanding antibiotic resistance: Challenges and solutions

Background: Antibiotic resistance (ABR) poses a critical threat to global health, with predictions indicating that by 2050, multi-drug resistant (MDR) infections could lead to approximately 10 million deaths annually, surpassing deaths from cancer and cardiovascular diseases. The overuse and misuse of antibiotics, particularly in agricultural settings, have exacerbated the issue. Aim: This review aims to provide healthcare staff with an understanding of the challenges posed by antibiotic resistance and explore potential solutions. Methods: A comprehensive literature review was conducted, analyzing historical and contemporary data on antibiotic discovery, resistance mechanisms, and current research initiatives aimed at addressing ABR. Results: Key findings indicate that the decline in new antibiotic development since the late 1980s, coupled with the rapid spread of resistance genes, has created an urgent need for novel therapeutic strategies. Recent research highlights promising compounds derived from natural sources, including marine fungi and Actinobacteria, which show potential against MDR pathogens. Conclusion: Immediate action is required to combat ABR, including improved antibiotic stewardship, public education, and increased funding for research into new antibiotics. Collaborative efforts among healthcare professionals, researchers, and policymakers are essential to address this escalating crisis.

A novel type of colistin resistance genes selected from random sequence space.

Antibiotic resistance is a rapidly increasing medical problem that severely limits the success of antibiotic treatments, and the identification of resistance determinants is key for surveillance and control of resistance dissemination. Horizontal transfer is the dominant mechanism for spread of resistance genes between bacteria but little is known about the original emergence of resistance genes. Here, we examined experimentally if random sequences can generate novel antibiotic resistance determinants de novo. By utilizing highly diverse expression libraries encoding random sequences to select for open reading frames that confer resistance to the last-resort antibiotic colistin in Escherichia coli, six de novo colistin resistance conferring peptides (Dcr) were identified. The peptides act via direct interactions with the sensor kinase PmrB (also termed BasS in E. coli), causing an activation of the PmrAB two-component system (TCS), modification of the lipid A domain of lipopolysaccharide and subsequent colistin resistance. This kinase-activation was extended to other TCS by generation of chimeric sensor kinases. Our results demonstrate that peptides with novel activities mediated via specific peptide-protein interactions in the transmembrane domain of a sensory transducer can be selected de novo, suggesting that the origination of such peptides from non-coding regions is conceivable. In addition, we identified a novel class of resistance determinants for a key antibiotic that is used as a last resort treatment for several significant pathogens. The high-level resistance provided at low expression levels, absence of significant growth defects and the functionality of Dcr peptides across different genera suggest that this class of peptides could potentially evolve as bona fide resistance determinants in natura.

Multiresistant Bacteria: Invisible Enemies of Freshwater Mussels

Freshwater mussels are among the most endangered groups of fauna anywhere in world. The indiscriminate use of antibiotics has led to the emergence of resistant strains. These antibiotic-resistant bacteria play a key role in increasing the risk allied with the use of surface water and in spread of resistance genes. Two endangered freshwater mussel species, Margaritifera margaritifera and Potomida littoralis, were sampled at 4 sampling sites along a 50km stretch of River Tua. Water samples were taken at same sites. Of the total of 135 isolates, 64.44% (39.26% from water and 25.19% from mussels) were coliform bacteria. Site T1, with the lowest concentration of coliform bacteria, and site T2 were the only ones where M. margaritifera was found. No E. coli isolates were found in this species and the pattern between water and mussels was similar. P. littoralis, which was present at T3/T4 sites, is the one that faces the highest concentration of bacterial toxins, which are found in treated wastewater effluents and around population centers. Sites T3/T4 have the isolates (water and mussels) with the highest resistance pattern, mainly to β-lactams. Water and P. littoralis isolates (T3/T4) showed resistance to penicillins and their combination with clavulanic acid, and to cephalosporins, precisely to a fourth generation of cephalosporin antibiotics. We discuss the conservation status and risk to water systems and the need for research into possible management measures. It is suggested that future studies on the health status of freshwater bivalves should incorporate measures to indicate bacteriological water quality.

Advances in Studies on Horizontal Gene Transfer Promoting the Evolution of Resistance Genes of Periodontal Pathogens

Horizontal gene transfer (HGT) plays an important role in bacterial evolution. HGT is an important way for bacteria to rapidly obtain genetic improvement. HGT promotes the transmission of biological characteristics such as virulence, antibiotic resistance and allometabolism in microorganisms. The bacteria in the mouth are abundant and abundant. Bacterial virulence gene (Virulence genes, VGs) and antibiotic resistance genes (Antibiotic resistance genes, ARGs) besides through vertical transmission by parental, also can through HGT in oral symbiotic species or genus within the transmission. HGT promotes the spread of virulence genes and resistance genes, becomes an important driving force for the adaptive evolution of oral microorganisms, increases the difficulty of the treatment of oral bacterial infectious diseases (periodontal disease, periradicular lesions, Periimplantitis, etc.), and brings serious harm to human oral health and even general health. With modern microbiology, genetics, molecular biology, the macro development of disciplines, such as genomics, electron microscope and laser confocal microscope, nucleic acid hybridization (especially the 16 sRNA gene sequencing) and other modern analysis technology has been widely applied in periodontal pathogens resistance genes, through the study of HGT way spread and made some progress. This paper will analyze and summarize the literature on the spread of resistance genes of common periodontal pathogens through HGT method in recent years, in order to provide reference for the follow-up study of resistance of periodontal pathogens, as well as for the solution of resistance of periodontal pathogens and the treatment of periodontal diseases.

Antimicrobial Drug-resistance Profile of Vibrio Parahaemolyticus isolated from Japanese Horse Mackerel (Trachurus Japonicus).

This study aimed at investigating antimicrobial resistance (AMR) profile of Vibrio parahaemolyticus (V. parahaemolyticus). The bacteria were isolated from wild-caught and farmed Japanese horse mackerel (Trachurus japonicus), and examined for the antimicrobial drug resistance. Furthermore, the serotype, and the genes of thermostable direct hemolysin (tdh) and cholera toxin transcriptional activator (toxR) of the isolates were investigated by using a serotype testing kit and PCR method. Eighty-eight and 126 V. parahaemolyticus strains were isolated from wild-caught and farmed Japanese horse mackerel, respectively. Ten and 18 distinct serotypes were detected from wild-caught and farmed Japanese horse mackerel. All strains were negative for tdh genes but positive for toxR genes. Resistances to ampicillin (ABP) and to both ABP and fosfomycin (FOM) were observed in 54 and 23 strains from the wild-caught fish, while those resistant strains from farm fish were 112 and 7 strains. Multidrug-resistance to three or four drugs including ABP was observed in one or two strains from the wild-caught fish.These results strongly suggest that the environmental exposure of antimicrobial drugs results in the spread of resistant genes in Japanese horse mackerel. This study highlights the need for monitoring the spread of resistance genes to the human intestinal flora as well as to other bacteria in the environment.

Prevalence of Aminoglycoside Resistance and Aminoglycoside Modifying Enzymes in Acinetobacter baumannii Among Intensive Care Unit Patients, Ismailia, Egypt

BackgroundAcinetobacter baumannii is an opportunistic pathogen that rapidly develops antibiotic resistance against commonly prescribed antimicrobial agents in hospitalized patients worldwide. Aminoglycosides are commonly used in the treatment of A. baumannii health care-associated infections (HAIs). Aminoglycosides resistance mechanisms are varied and commonly involve production of aminoglycoside-modifying enzymes (AME) and efflux systems.AimThis study aimed to provide an insight into the frequency of genes encoding AME in A. baumannii strains isolated from different clinical specimens in intensive care units (ICU).MethodologyA total of 52 multidrug-resistant (MDR) A. baumannii strains were isolated from ICU, Suez Canal University Hospitals. Species identification and antibiotics susceptibility testing were done by the automated system VITEK 2. The genes encoding AME were detected by PCR.ResultsAminoglycosides resistance (amikacin, gentamicin and tobramycin) was observed in 35 isolates (67.3%). We found that aacC1 gene was the predominant AME resistance gene among A. baumannii isolates, detected in 14 isolates (40%), aphA6 in 11 isolates (31.4%) and addA1 in 5 isolates (14.2%). We found 5 isolates containing 2 AME genes, 3 of them with aacC1 and aphA6 and the remaining 2 with both aacC1 and aadA1 genes. Nearly, 5 isolates (14.2%) were negative for all AME resistance genes.ConclusionOur study indicated that AME encoding genes are predominant in A. baumannii strains in our region which stressed on the importance of preventive measures to control spreading of resistance genes.

Genomic characterization of clinical Enterobacter roggenkampii co-harbouring blaIMP-1- and blaGES-5-encoding IncP6 and mcr-9-encoding IncHI2 plasmids isolated in Japan

ObjectivesThe spread of carbapenemase-producing Enterobacterales (CPE) with colistin resistance is a critical public health issue. We genetically characterized the clinical isolate Enterobacter roggenkampii OIPH-N260, which harboured carbapenemase genes blaIMP-1 and blaGES-5 with multiple resistance genes, including mcr-9 and blaCTX-M-9. MethodsThis isolate was characterized by whole-genome sequencing, comparative analysis of resistance plasmids, susceptibility tests, bacterial conjugation, S1-nuclease digested pulsed-field-gel electrophoresis, and Southern blot hybridization. ResultsThe OIPH-N260 isolate exhibited resistance to most β-lactams and colistin. It co-harboured two resistance plasmids, the blaIMP-1- and blaGES-5-encoding IncP6 plasmid pN260-3 and mcr-9- and blaCTX-M-9-encoding IncHI2 plasmid pN260-1. The comparative analysis of pN260-3 indicated that a unique blaIMP-1-surrounding region was inserted into the blaGES-5-encoding plasmid with the mobile element IS26, which plays an important role in the spread of resistance genes. pN260-1 did not possess the mcr-9 expression regulative gene qseBC. Both plasmids were transferable into other bacterial species via conjugation. ConclusionsThis is the first study to report not only a blaIMP-1 and blaGES-5 co-encoding plasmid, but also the co-harbouring of another plasmid carrying mcr-9 and blaCTX-M-9 in Enterobacter cloacae complex. The development of advanced resistance via IS26-mediated insertion and the co-harbouring of resistance plasmids highlights the need to monitor for resistance genes in CPE.

Characteristic of extended-spectrum-B-lactamase (ESBL) Producing Klebsiella pneumoniae at tertiary referral hospital in South Sulawesi, Indonesia

Background: The extensive and irrational use of antibiotics had led to the emergence of Multi Drug Resistance worldwide. World Health Organization (WHO) placed ESBL producing Klebsiella pneumoniae in the Priority Pathogen List as one of the first priority that pose great threat to human health. It has built-in abilities to resist treatment and can pass along genetic material that allows other bacteria to become drug-resistant as well. Little were known about the local epidemiology of ESBL producing K.pneumoniae in Indonesia, especially South Sulawesi region. Therefore we intend to discover the ESBL producing K.pneumoniae with both phenotype and genotype characteristics. Methods and materials: We collected clinical specimens from patients admitted at Dr.Wahidin Sudirohusodo Hospital Makassar within January to June 2019. We conducted routine microbial identification to get the K.pneumoniae isolates. The ESBL phenotypes were tested using VITEK 2 automated system (Biomeriuex) and the molecular characteristic were tested with multiplex PCR method using blaTEM, blaSHV and blaCTX-M. Results: Almost 30% of K.pneumoniae were identified from total positive cultures of inpatients clinical specimens. High proportion of ESBL producing K.pneumoniae were documented in this study (46 out of 56) phenotypically. Molecular test results on CTX-M as the predominant ESBL gene (50 out of 56), followed by TEM-164 (44 out of 56) and SHV (26 out of 56). We found there is discrepancy between phenotype and genotype results. Most of the isolates which missing the ESBL phenotype (40%) were causing sepsis. Conclusion: We proposed an insight that MDR K.pneumoniae especially ones producing ESBL compare to Non ESBL was high in proportion at Dr.Wahidin Sudirohusodo Hospital. It should alarmed us the importance of this knowledge in order to execute proper treatment for the patients. Nevertheless, the need to emphasize on Infection Prevention and Control to stop the spread of resistance genes together with Antimicrobial Stewardship in Hospital based is prominent.

Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures.

Plasmids are the key element in horizontal gene transfer in the microbial community. Recently, a large number of experimental and computational methods have been developed to obtain the plasmidomes of microbial communities. Distinguishing transmissible plasmid sequences, which are derived from conjugative or at least mobilizable plasmids, from non-transmissible plasmid sequences in the plasmidome is essential for understanding the diversity of plasmids and how they regulate the microbial community. Unfortunately, due to the highly fragmented characteristics of DNA sequences in the plasmidome, effective identification methods are lacking. In this work, we used information entropy from information theory to assess the randomness of synonymous codon usage over 4424 plasmid genomes. The results showed that for all amino acids, the choice of a synonymous codon in conjugative and mobilizable plasmids is more random than that in non-transmissible plasmids, indicating that transmissible plasmids have different sequence signatures from non-transmissible plasmids. Inspired by this phenomenon, we further developed a novel algorithm named PlasTrans. PlasTrans takes the triplet code sequences and base sequences of plasmid DNA fragments as input and uses the convolutional neural network of the deep learning technique to further extract the more complex signatures of the plasmid sequences and identify the conjugative and mobilizable DNA fragments. Tests showed that PlasTrans could achieve an AUC of as high as 84–91%, even though the fragments only contained hundreds of base pairs. To the best of our knowledge, this is the first quantitative analysis of the difference in sequence signatures between transmissible and non-transmissible plasmids, and we developed the first tool to perform transferability annotation for DNA fragments in the plasmidome. We expect that PlasTrans will be a useful tool for researchers who analyse the properties of novel plasmids in the microbial community and horizontal gene transfer, especially the spread of resistance genes and virulence factors associated with plasmids. PlasTrans is freely available via https://github.com/zhenchengfang/PlasTrans

Evolutionary Approaches to Combat Antibiotic Resistance: Opportunities and Challenges for Precision Medicine.

The rise of antimicrobial resistance (AMR) in bacterial pathogens is acknowledged by the WHO as a major global health crisis. It is estimated that in 2050 annually up to 10 million people will die from infections with drug resistant pathogens if no efficient countermeasures are implemented. Evolution of pathogens lies at the core of this crisis, which enables rapid adaptation to the selective pressures imposed by antimicrobial usage in both medical treatment and agriculture, consequently promoting the spread of resistance genes or alleles in bacterial populations. Approaches developed in the field of Evolutionary Medicine attempt to exploit evolutionary insight into these adaptive processes, with the aim to improve diagnostics and the sustainability of antimicrobial therapy. Here, we review the concept of evolutionary trade-offs in the development of AMR as well as new therapeutic approaches and their impact on host-microbiome-pathogen interactions. We further discuss the possible translation of evolution-informed treatments into clinical practice, considering both the rapid cure of the individual patients and the prevention of AMR.