Dissemination Of Resistance Genes Research Articles

Structural diversity of the ISCR2-mediated rolling-cycle transferable unit carrying tet(X4)

BackgroundMobile tigecycline-resistance gene tet(X) variants have emerged as diverse pathogens from animal, human as well as their associated environments, which could potentially threaten public health. The insertion sequence, ISCR2, carries tet(X4) for horizontal transfer by rolling-cycle (RC) transposition. However, the diversity of ISCR2 and tet(X4) isolated from different sources is largely unknown. MethodsThe tet(X4)-carrying isolates were collected from human and livestock in several multiple regions of China. The whole genomic sequences of these isolates were either obtained from NCBI GenBank or determined by Illumina Hiseq 2500 and the MinION platform. The intact transposon region, ISCR2-tet(X4)-ISCR2, observed in a small number of isolates as the reference sequence to construct the transposon phylogeny. The diversity of the genetic environments of all ISCR2-tet(X4) elements were analyzed. ResultsA 2760-bp element encompassing the tet(X4)-hydrolase-encoding gene, catD, located between two ISCR2 elements was highly conserved in all isolates and could form an RC transposable unit (RC-TU). ISCR2 could also capture more resistance genes and formed a larger RC-TU base on RC transposition. However, the ISCR2-mediated RC-TUs were constantly truncated and inserted by other IS elements, indicating frequent recombination events. Of these elements, IS26 disrupted both the upstream and downstream ISCR2-mediated RC-TUs, indicating that IS26 captured tet(X4), thus leading to a wider spread of tet(X4). ConclusionsThese results confirmed the critical role of ISCR2 for dissemination and co-transmission of tet(X4) and other resistance genes. More effort is needed to monitor the variation tendencies of tet(X4)-carrying mobile elements and determine the driving factors for disseminating transferable tigecycline resistance.

Co-selective Pressure of Cadmium and Doxycycline on the Antibiotic and Heavy Metal Resistance Genes in Ditch Wetlands.

Abuse of heavy metals and antibiotics results in the dissemination of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Ditch wetlands are important sinks for heavy metals and antibiotics. The relationships between bacterial communities and MRG/ARG dissemination under dual stresses of heavy metals and antibiotics remain unclear. The responses of MRGs and ARGs to the co-selective pressure of cadmium (Cd) and doxycycline (DC) in ditch wetlands were investigated after 7-day and 84-day exposures. In ecological ditches, residual rates of Cd and DC varied from 0.4 to –5.73% and 0 to –0.61%, respectively. The greatest total relative abundance of ARGs was observed in the Cd 5 mg L–1 + DC 50 mg L–1 group. A significant level of DC (50 mg L–1) significantly reduced the total relative abundances of MRGs at a concentration of 5 mg L–1 Cd stress. Redundancy analysis indicated that Cd and DC had strong positive effects on most ARGs and MRGs after a 7-day exposure. Meanwhile, the class 1 integron gene (intI1) exhibited strong positive correlations with most ARGs and cadmium resistance genes (czcA) after an 84-day exposure. Network analysis showed that Acinetobacter and Pseudomonas were the potential dominant host genera for ARGs and MRGs, and tetracycline resistance genes (tetA), czcA, and intI1 shared the same potential host bacteria Trichococcus after an 84-day exposure.

Impact of a Regulation Restricting Critical Antimicrobial Usage on Prevalence of Antimicrobial Resistance in Escherichia coli Isolates From Fecal and Manure Pit Samples on Dairy Farms in Québec, Canada.

To tackle antimicrobial resistance (AMR), one of the major health threats of this century, the World Health Organization (WHO) endorsed a global action plan in 2015. This plan calls countries to develop national actions to address AMR. The province of Québec, Canada, adopted a new regulation on the 25th of February 2019, to limit the use in food animals of antimicrobials of very high importance in human medicine. We aimed to establish the impact of this regulation by comparing the AMR situation in dairy cattle in Québec ~2 years before and 2 years after its introduction. We sampled calves, cows, and the manure pit in 87 farms. Generic and putative ESBL/AmpC E. coli were tested for susceptibility to 20 antimicrobials. Logistic regression was used to investigate whether the probability of antimicrobial resistance differed between isolates obtained from the pre and post regulation periods by sample type (calves, cows, manure pit) and in general. To identify AMR genes dissemination mechanisms, we sequenced the whole genome of 15 generic isolates. In the generic collection, at the herd level, the proportion of multidrug resistant (MDR) isolates, decreased significantly from 83 to 71% (p = 0.05). Folate inhibitor and aminoglycoside resistances demonstrated a significant decrease. However, when analyzed by sample type (calves, cows, manure pit), we did not observe a significant AMR decrease in any of these categories. In the ESBL/AmpC collection, we did not detect any significant difference between the two periods. Also, the general resistance gene profile was similar pre and post regulation. We identified both clonal and plasmidic dissemination of resistance genes. In conclusion, as early as 2 years post regulation implementation, we observed a significant decrease in MDR in the dairy industry in Quebec in the generic E. coli collection with folate inhibitor and aminoglycoside resistances showing the most significant decrease. No other significant decreases were yet observed.

Recombination events that occur in a poxtA-carrying Enterococcus faecium during the conjugation process.

To investigate transferability of the poxtA-carrying plasmids in Enterococcus faecium and the mechanism of recombination that occurs during the conjugation process. MICs were determined by broth microdilution. Transferability of the poxtA-carrying plasmids in E. faecium was investigated by conjugation. The mechanism of recombination that occurred during the conjugation process was explored by S1-PFGE and WGS. E. faecium strain Fac90 carries two plasmids, designated pFac90-154 and pFac90-54, respectively. Six transconjugants with different characteristics were obtained. In transconjugant T90-1, a plasmid-chromosome fusion event led to the integration of plasmid pFac90-154 from the donor E. faecium strain Fac90 into the chromosomal DNA of the recipient strain Enterococcus faecalis JH2-2. In transconjugants T90-2, -3 and -4, losses or additions of different-sized plasmid segments most likely occurred due to IS1216-mediated recombination. In transconjugants T90-5 and -6, two large plasmids with sizes of 101 656 and 149 526 bp were formed by plasmid fusion. To the best of our knowledge, this is the first report showing the integration of pFac90-154 from E. faecium Fac90 into the chromosomal DNA of recipient E. faecalis JH2-2 via homologous recombination. Besides, we showed that five new plasmid types were formed by genetic rearrangements. These recombination events resulted simultaneously in the formation of various types of mosaic plasmids with multiple resistance genes and/or conjugation characteristics, which might promote the transmission of diverse plasmids encoding resistance genes among enterococci. Thus, these data significantly expand our knowledge regarding conjugative events, establishing a dual role of conjugation in both dissemination of resistance genes and plasmid evolution.

Occurrence of Antimicrobial Resistant Escherichia coli and Staphylococcus sp. in Faecal Samples of Wild Birds

Background: Microbial resistance to antibiotics is a worldwide problem in human and veterinary medicine. The principal risk factor for an increase in this situation is the extensive use of antibiotics leading to the dissemination of resistant bacteria and resistance genes. Bacteria from Wild birds are important with regard to antibiotic resistance due to diverse ecology and as reservoir of antibiotic resistant bacterial genes and potential spreaders. Methods: In the present study, a total of total 75 faecal swabs from captive and free ranging wild birds were obtained for isolation and identification of E. coli and Staphylococcus sp. They were detected for presence of antimicrobial resistant drugs, six each, by using standard kirby- beaur disc diffusion test. Result: Isolation rate of E coli and Staphylococcus sp. was 77% each respectively. Antimicrobial susceptibility profile revealed resistance in E. coli was 25% and in Staphylococcus sp. 10%. Most resistant antimicrobial in E. coli and Staphylococcus sp. was Cotrimoxazole (22%) and Clindamycin (8.6%) respectively. Presence of resistance in wild birds’ species is an alarming situation as these are capable to transmitting resistant gene either vertically or horizontally. Regulating the usage of Antimicrobials in livestock and humans is the need of the hour.

RW-BP100-4D, a Promising Antimicrobial Candidate With Broad-Spectrum Bactericidal Activity.

With the rapid emergence and dissemination of antimicrobial resistance (AMR) genes in bacteria from animal, animal-derived food and human clinic, it is of great significance to develop new approaches to combat the multidrug-resistant bacteria. This study presented a short linear antimicrobial peptide RW-BP100-4D, which was derived from RW-BP100 (RRLFRRILRWL-NH2) by transforming the N-terminal 4th amino acid from L- to D-enantiomer. This modification remarkably reduced the peptide cytotoxicity to mammalian cells, as indicated by hemolytic and cytotoxicity assays. Meanwhile, the antimicrobial activity of RW-BP100-4D was improved against a more variety of Gram-positive and Gram-negative bacteria (sensitive and resistant) as well as fungi. Also, RW-BP100-4D showed strong in vitro anti-biofilm activity in a concentration-dependent manner, including inhibition of the biofilm-formation and dispersion of the mature biofilms of Staphylococcus aureus. RW-BP100-4D could be efficiently uptaken by bovine mammary epithelial cells (MAC-T) cells to eliminate the intracellular S. aureus ATCC29213 and Salmonella enterica ATCC13076. Moreover, RW-BP100-4D was highly effective in food disinfection of multiple bacterial contamination (including S. aureus, Listeria monocytogenesis, Escherichia coli O157: H7, Campylobacter jejuni, S. enterica, and Shewanella putrefaction, 3.61 ± 0.063 log reduction) on chicken meat, and could kill 99.99% of the methicillin-resistant Staphylococcus aureus (MRSA) strain in the mouse skin infection model. In summary, RW-BP100-4D is a promising antimicrobial candidate for application on food disinfection and local infection treatment. However, the protease-sensitivity of RW-BP100-4D and toxic effect at higher doses reduced the therapeutic effect of the candidate peptide in vivo and should be improved in the future studies.

Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern.

Water supply reservoirs form one of the critical drinking water resources. Their water quality directly affects human health. However, reservoir sediments have not received adequate attention in antibiotic resistance genes (ARGs) dissemination, though they reflect long-term ARGs contamination of water supply reservoirs. Moreover, the physicochemical parameters in water supply reservoir sediments are generally better than those in the other media. Thus, the main ARGs biotic drivers of the media would demonstrate their unique characteristics. In this study, sediment samples were collected from 10 water supply reservoirs in central China, and the antibiotic resistomes were determined with the metagenomic method. As revealed from the results, 174 ARGs (18 ARG types) were detected in the reservoir sediment. Besides, multidrug-, sulfonamide-, and vancomycin-ARGs were the dominant ARGs in the sediment samples. The macrolide-resistant Microcystis was prevalent (100% detection frequency with 0.35% average percentage) in reservoir sediments and posed potential risks to human health. Furthermore, the results of the Mantel test and VPA demonstrated that mobile genetic elements (MGEs) were the more essential biotic drivers in ARG contents of reservoir sediments rather than the bacteria community.

Emergence and Genomic Characterization of a KPC-2-, NDM-1-, and IMP-4-Producing Klebsiella michiganensis Isolate.

A rectal swab sample was collected from a patient with Guillain–Barré syndrome and enriched in lysogeny broth. Carbapenem-resistant bacteria were selected by China Blue agar plates containing 0.3 μg/ml meropenem. Carbapenemase-producing Klebsiella michiganensis was identified and characterized by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), immune colloidal gold technique, a conjugation experiment, PCR analysis, and antimicrobial susceptibility testing. The genome of K. michiganensis was determined by whole genome sequencing. Antimicrobial susceptibility testing showed that the K. michiganensis was resistant to imipenem, meropenem, ertapenem, cefmetazole, ceftazidime, cefotaxime, piperacillin/tazobactam, sulbactam/cefoperazone, ceftazidime/avibactam, cefepime, and aztreonam while susceptible to polymyxin B, ciprofloxacin, tigecycline, and amikacin. Immune colloidal gold technique suggested that this strain co-produced three different carbapenemases [Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), and Imipenem (IMP)]. Whole genome sequencing analysis indicated that this strain belonged to ST91, and blaKPC–2, blaNDM–1, and blaIMP–4 were carried on different conjugative plasmids. Besides, the co-existence and transferability of blaKPC–2, blaNDM–1, and blaIMP–4 in K. michiganensis facilitates the potential horizontal dissemination and nosocomial spread of resistance genes among multidrug-resistant organisms.

Roles of Proteins Containing Immunoglobulin-Like Domains in the Conjugation of Bacterial Plasmids.

ABSTRACTHorizontal transfer of bacterial plasmids generates genetic variability and contributes to the dissemination of the genes that enable bacterial cells to develop antimicrobial resistance (AMR). Several aspects of the conjugative process have long been known, namely, those related to the proteins that participate in the establishment of cell-to-cell contact and to the enzymatic processes associated with the processing of plasmid DNA and its transfer to the recipient cell. In this work, we describe the roles of newly identified proteins that influence the conjugation of several plasmids. Genes encoding high-molecular-weight bacterial proteins that contain one or several immunoglobulin-like domains (Big) are located in the transfer regions of several plasmids that usually harbor AMR determinants. These Big proteins are exported to the external medium and target two extracellular organelles: the flagella and conjugative pili. The plasmid gene-encoded Big proteins facilitate conjugation by reducing cell motility and facilitating cell-to-cell contact by binding both to the flagella and to the conjugative pilus. They use the same export machinery as that used by the conjugative pilus components. In the examples characterized in this paper, these proteins influence conjugation at environmental temperatures (i.e., 25°C). This suggests that they may play relevant roles in the dissemination of plasmids in natural environments. Taking into account that they interact with outer surface organelles, they could be targeted to control the dissemination of different bacterial plasmids carrying AMR determinants.IMPORTANCE Transmission of a plasmid from one bacterial cell to another, in several instances, underlies the dissemination of antimicrobial resistance (AMR) genes. The process requires well-characterized enzymatic machinery that facilitates cell-to-cell contact and the transfer of the plasmid. Our paper identifies novel plasmid gene-encoded high-molecular-weight proteins that contain an immunoglobulin-like domain and are required for plasmid transmission. They are encoded by genes on different groups of plasmids. These proteins are exported outside the cell. They bind to extracellular cell appendages such as the flagella and conjugative pili. Expression of these proteins reduces cell motility and increases the ability of the bacterial cells to transfer the plasmid. These proteins could be targeted with specific antibodies to combat infections caused by AMR microorganisms that harbor these plasmids.

Effect of aromatic oils on the expression of some virulence-associated and antimicrobial resistance genes of Escherichia coli isolated from broilers.

Objectives:This study aimed to prove the effects of Escherichia coli isolates isolated from diseased broilers to form biofilms, describe their antimicrobial sensetivity, and determine the effect of allicin and cinnamon essential oils on the expression of some genes (fimH, int1, and luxS) through quantitative polymerase chain reaction (q-PCR).Materials and Methods:140 samples were obtained from diseased broilers in Beni-Suef Governorate, Egypt. These samples were examined by conventional bacteriology methods to detect the causative agent. The antimicrobial susceptibility of the isolated bacteria was assessed using the disc diffusion method, The ability of yeast extract-casamino acids Congo Red Agar to generate phenotypic biofilms was next tested. The presence of resistance and virulence genes in some multidrug resistant isolates was genotypically investigated. The antibacterial effects of allicin and cinnamon oil were evaluated against the growth of multidrug-resistant E. coli. Finally, q-PCR was utilized to assess changes in some genes’ expression.Results:Escherichia coli was isolated from 61 samples (43.6%). An antimicrobial susceptibility test revealed that multidrug-resistance (MDR) (could resist more than three antimicrobial classes) E. coli prevalence was 100%. 40.8% of isolates phenotypically produce biofilms. The detection of resistance and virulence genes by PCR showed that all tested isolates carry aadB, fimH, int1, qnrS, and luxS genes, while only 40% harbor iss genes. q-PCR showed that after treatment with allicin and cinnamon oils, gene expression went down.Conclusion:This investigation highlights that E. coli showed resistance against most of the tested antimicrobials; all isolates were MDR. The study showed wide dissemination of virulence and resistance genes among E. coli. Allicin and cinnamon oils have antimicrobial activities and could be used as alternatives to synthetic antimicrobial agents.

Viral Community in Landfill Leachate: Occurrence, Bacterial Hosts, Mediation Antibiotic Resistance Gene Dissemination, and Function in Municipal Solid Waste Decomposition

Viral Community in Landfill Leachate: Occurrence, Bacterial Hosts, Mediation Antibiotic Resistance Gene Dissemination, and Function in Municipal Solid Waste Decomposition

Viral Community in Landfill Leachate: Occurrence, Bacterial Hosts, Mediation Antibiotic Resistance Gene Dissemination, and Function in Municipal Solid Waste Decomposition

Viral Community in Landfill Leachate: Occurrence, Bacterial Hosts, Mediation Antibiotic Resistance Gene Dissemination, and Function in Municipal Solid Waste Decomposition

Genomic characterization of multidrug-resistant extraintestinal pathogenic Escherichia coli isolated from grain culture soils

Multidrug-resistant (MDR) Escherichia coli , mainly extraintestinal pathogenic E. coli (ExPEC), has been widely reported in infections worldwide. In agricultural soils, manure is a hotspot for the dissemination of antimicrobial resistance genes (ARGs) and pathogenic bacteria; however, MDR bacteria have also been reported in soils with no history of manure use. In addition, cross-resistance and co-resistance have been described as responsible for the metal-driven selection of bacteria resistant to antimicrobials. Therefore, the aim of this study was to analyze three MDR E. coli isolates obtained from Brazilian grain culture soil samples with no history of manure use by whole-genome sequencing. The MDR E. coli isolates were recovered from soils from corn and coffee fields, and presented resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, and dihydrofolate reductase inhibitor. Resistome analysis showed ARGs to several antimicrobials ( i.e. , β-lactams, tetracyclines, aminoglycosides, sulphonamides, trimethoprim, phenicols, fosfomycin, and macrolides) as well as several metal resistance genes and antibacterial biocide resistance genes. In addition, known mutations in quinolone-resistance-determining regions of GyrA (Ser83Leu and Asp87Asn), ParE (Ser458Thr), and ParC (Ser80Ile) were also detected. Virulome analysis showed the presence of virulence genes ( lpfA , mcmA , gad , mchF , iroN , cma , and iss ) associated with ExPEC. Multidrug-resistant ExPEC isolates were assigned to phylogenetic group B1. The presence of MDR B1-ExPEC in soil samples shows the ability of these isolates to survive in soils. This study reports for the first time some sequence types ( i.e. , ST345, ST448, and ST1146) of MDR E. coli in Brazilian soils. Therefore, these findings contribute to the monitoring of antimicrobial resistance and surveillance studies based on whole-genome sequencing worldwide.

Pseudomonas putida group species as reservoirs of mobilizable Tn402-like class 1 integrons carrying blaVIM-2 metallo-β-lactamase genes.

The Pseudomonas putida group (P. putida G) is composed of at least 21 species associated with a wide range of environments, including the clinical setting. Here, we characterized 13 carbapenem-resistant P. putida G clinical isolates bearing class 1 integrons/transposons (class 1 In/Tn) carrying blaVIM-2 metallo-β-lactamase gene cassettes obtained from hospitals of Argentina. Multilocus sequencing (MLSA) and phylogenetic analyses based on 16S rDNA, gyrB and rpoD sequences distinguished 7 species among them. blaVIM-2 was found in three different cassette arrays: In41 (blaVIM-2-aacA4), In899 (only blaVIM-2), and In528 (dfrB1-aacA4-blaVIM-2). In41 and In899 were associated with complete tniABQC transposition modules and IRi/IRt boundaries characteristic of the Tn5053/Tn402 transposons, which were designated Tn6335 and Tn6336, respectively. The class 1 In/Tn element carrying In528, however, exhibited a defective tni module bearing only the tniC (transposase) gene, associated with a complete IS6100 bounded with two oppositely-oriented IRt end regions. In some P. putida G isolates including P. asiatica, P. juntendi, P. putida G/II, and P. putida G/V, Tn6335/Tn6336 were carried by pLD209-type conjugative plasmids capable of self-mobilization to P. aeruginosa or Escherichia coli. In other isolates of P. asiatica, P. putida G/II, and P. monteiliieilii, however, these blaVIM-2-containing class 1 In/Tn elements were found inserted into the res regions preceding the tnpR (resolvase) gene of particular Tn21 subgroup members of Tn3 transposons. The overall results reinforce the notion of P. putida G members as blaVIM-2 reservoirs, and shed light on the mechanisms of dissemination of carbapenem resistance genes to other pathogenic bacteria in the clinical setting.

Proteus mirabilis carrying NTEKPC-IId, blaNDM-1, blaOXA-10, aph(3')-VI, qnrD1 and IncQ and Col3M plasmids from a hospital in Recife-PE, Brazil

The present study objective to characterize the clinical aspects of a patient infected with two strains of P. mirabilis and the presence of resistance determinants in the two isolates from a patient at a public hospital in Recife-PE, Brazil. The total DNA of the isolates was extracted and submitted to PCR and amplicon sequencing for the investigation of resistance genes, blaKPC, blaOXA-10, blaOXA-23, blaOXA-48, blaOXA-58, blaVIM, blaIMP, blaSPM, blaGES, blaNDM, qnrD and aac(6')-Ib). Isolate P21-A2 harbored the aac(6')-Ib, blaOXA-10 and qnrD genes. One of the isolates, P20-A2, was selected for plasmid DNA sequencing. The results showed that the patient developed multiple infections with various pathogens including two strains of P. mirabilis. The patient was hospitalized for 103 days, had septic shock of skin, abdominal, pulmonary and ulcer focus, and died. Isolate P20-A2 harbored the genes blaNDM, qnrD, aph(3')-VI, blaKPC and blaOXA-10, and plasmids IncQ and Col3M, together with NTEKPC-IId. To our knowledge, this is the first report of P. mirabilis harboring NTEKPC-IId. Although P. mirabilis is standing out as a cause of nosocomial infections and a resistant multidrug pathogen, this species is still neglected, the emergence of these P. mirabilis isolates harboring aforementioned resistance determinants and the plasmids IncQ and Col3M demonstrate the potential for dissemination of important resistance genes, mainly in the case of P. mirabilis.

Characterization of Aminoglycoside Modifying Enzymes Producing E. coli and Klebsiella pneumoniae Clinical Isolates

Antimicrobial resistance gene profile characterization and dissemination offer useful detail on the possible challenge in treating bacteria. The development of aminoglycoside modifying enzymes (AMEs) is considered as the primary mechanism of resistance to aminoglycosides, in addition to the 16S rRNA methylases. This study aimed at isolation and characterization of aminoglycosides resistant clinical isolates of enterobacteriaceae family from different clinical samples. Over a period of 24 months, thirty samples were collected and 49 clinical isolates of E. coli [n=25], Klebsiella [n=13], Enterobacter species (n=7) and Proteus species (n=4) were isolated from Egyptian clinical laboratories. The identities of the cultures were confirmed following standard microbiological procedures. Resistance of the isolates to aminoglycosides was determined by the disc diffusion method and isolates with highest resistance (n=9) were selected and investigated for 16S rRNA methylase and AMES encoding genes by polymerase chain reaction (PCR) and sequencing. In general, aminoglycoside resistance was found in 95% of the isolates; the isolates displayed the highest rate of resistance to netilmicin (75%) and kanamycin (55%), while resistance to gentamycin (18%) and tobramycin (16%) was low. A total of 9 isolates have the highest aminoglycoside resistant rate, showed the highest appearance for aac(6′)-Ib as well as ant (3″)-Ia resistant genes, with aac (3)-II (44%) and ant (4′)-IIb (34%) following closely. The high prevalence of AMEs observed among resistant isolates in this study suggests the urgent need for more efficient treatment designs to mitigate the selection burden as well as improved care of patients who have been infected with these drug-resistant organisms.

Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa.

Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.

Dissemination of antibiotic resistance under antibiotics pressure during anaerobic co-digestion of food waste and sludge: Insights of driving factors, genetic expression, and regulation mechanism

This study revealed the effects and regulation mechanisms on antibiotic resistance genes (ARGs) dissemination during anaerobic co-digestion (AcoD) of food waste and sludge under the exposure of tetracycline, sulfamethoxazole (SMZ) and erythromycin (ERY). Results indicated antibiotics significantly increased the abundance of ARGs, and selectively enriched integron gene, suggesting antibiotics promoted the dissemination of ARGs. Procrustes analysis indicated that bacterial community, integrons and physicochemical properties displayed significant correlations with ARGs, and they respectively contributed 10.61%, 6.94% and 2.97% of explanations on ARGs variation. Especially, the maximum combined contribution (48.6%) of bacterial community and integrons, implying their significances on ARGs alteration. Metatranscriptomic analysis further demonstrated antibiotics upregulated the expressions of total ARGs and virulence factors, raising potential risks. The proposed mechanisms for ARGs dissemination facilitated by antibiotics might be attributed to the changes of ARGs-regulated functions for inducing DNA/cell damage and DNA conjugation during AcoD.

Prevalence of class I, II and III integrons in multidrug-resistant and carbapenem-resistant Pseudomonas aeruginosa clinical isolates

Integrons are mobile genetic elements located on transposons, plasmids and bacterial chromosomes. These elements play a key role in spreading resistance gene cassettes to various disinfectants and antibiotics and facilitate the global antibiotic resistance crisis. The present study was aimed to evaluate the prevalence of class I, II and III integrons in multidrug-resistant (MDR) and carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains isolated from patients referring to Ardabil hospitals. A total of 103 confirmed P. aeruginosa clinical isolates were included in this study (collected between June 2019 and April 2021). Antibiotic resistance pattern was assessed using Kirby-Bauer disk diffusion method on Mueller–Hinton agar. The presence of intI1, intI2 and intI3 genes was detected using the set of specific primers by polymerase chain reaction (PCR) assay. The total frequency of class I integron gene was 58.3% in P. aeruginosa isolates. No class II and III integrons were detected in P. aeruginosa isolates. The prevalence of MDR P. aeruginosa strains was 54.3% and the rate of class I integron was significantly higher in MDR P. aeruginosa than non-MDR isolates (76.7% vs. 23.3%) (p < 0.05). Additionally, the frequency of class I integron gene among carbapenem-resistant P. aeruginosa strains was as follows: doripenem 44.7%, imipenem 85.5% and meropenem 62.7% (p < 0.05). Our results revealed that class I integron was the most prevalent integrons among clinical isolates of drug-resistant P. aeruginosa in Ardabil hospitals. These integrons seem to play a significant role in dissemination of drug resistance genes and the emergence of antibiotic-resistant strains, particularly MDR and carbapenem-resistant ones.

Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems.

Antibiotic resistance is the principal mechanism of an evergrowing bacterial threat. Antibiotic residues in the environment are a major contributor to the spread of antibiotic resistance genes (ARGs). Subinhibitory concentrations of antibiotics cause bacteria to produce reactive oxygen species (ROS), which can lead to mutagenesis and horizontal gene transfer (HGT) of ARGs; however, little is known about the mitigation of ARG dissemination through ROS removal by antioxidants. In this study, we examine how antioxidant-producing microorganisms inoculated in replicate activated sludge systems can biologically mitigate the dissemination of ARGs. Through quantitative polymerase chain reaction (qPCR), we showed that antioxidant-producing microorganisms could decrease the persistence of the RP4 plasmid and alleviate enrichment of ARGs (sul1) and class 1 integrons (intl1). Metagenomic sequencing identified the most diverse resistome and the most mutated Escherichia coli ARGs in the reactor that contained antibiotics but no antioxidant-producing microorganisms, suggesting that antioxidant-producing microorganisms mitigated ARG enrichment and mutation. Host classification revealed that antioxidant-producing microorganisms decreased the diversity of ARG hosts by shaping the microbial community through competition and functional pathway changes. Conjugative experiments demonstrated that conjugative transfer of ARGs could be mitigated by coculture with antioxidant-producing microorganisms. Overall, this is a novel study that shows how ARG enrichment and HGT can be mitigated through bioaugmentation with antioxidant-producing microorganisms.