Integrons and gene cassettes in the enterobacteriaceae

A TaqMan real-time PCR assay for detection of qacEΔ1 gene in Gram-negative bacteria

The transfer of biocide and antibiotic resistance genes by mobile genetic elements is the most common mechanism for rapidly acquiring and spreading resistance among bacteria. The qacEΔ1 gene confers the resistance to quaternary ammonium compounds (QACs). It has also been considered a genetic marker for the presence of class 1 integrons associated with multidrug-resistant (MDR) phenotypes in Gram-negative bacteria. In this study, a TaqMan real-time PCR assay was developed to detect the qacEΔ1 gene in Gram-negative bacteria. The assay has a detection limit of 80 copies of the qacEΔ1 gene per reaction. No false-positive or false-negative results have been observed. Simultaneous amplification and detection of the 16S rRNA gene is performed as an endogenous internal amplification control (IAC). The TaqMan real-time PCR assay developed is a rapid, sensitive, and specific method that could be used to monitor resistance to QACs, the spread of class 1 integrons, and the prediction of associated MDR phenotypes in Gram-negative bacteria.

Presence of integrons and their correlation with multidrug resistance in Salmonella enterica serovar Typhimurium: Exploratory systematic review

In Salmonella enterica serovar Typhimurium (Typhimurium), multidrug resistance is associated with integrons carrying resistance genes dispersed by mobile genetic elements. This exploratory systematic review sought to identify integron types and their resistance genes in multidrug resistance Typhimurium isolates. We used Medline, PubMed, SciELO, ScienceDirect, Redalyc, and Google Scholar as motor searchers for articles in Spanish or English published between 2012 and 2020, including the keywords “integrons”, “antibiotic resistance”, and “Salmonella Typhimurium”. We included 38 articles reporting multidrug resistance up to five antibiotic families. Class 1 integrons with aadA2 and blaPSE-1 gene cassettes were predominant, some probably related to the Salmonella genomic island 1. We did not find studies detailing class 1 and 2 integrons in the same isolate, nor class 3 integrons reported. The presence of integrons largely explains the resistance profiles found in isolates from different sources in 15 countries.

Stenotrophomonas maltophilia outbreak originating from a pull-out faucet in a pediatric intensive care unit in Turkey: Insights from clinical records and molecular typing

BACKGROUND

Nosocomial Stenotrophomonas maltophilia-related cases are rising and pose a threat to immunocompromised patients. Twelve patients from our pediatric intensive care unit (PICU) presented with S maltophilia-associated bloodstream infection.

METHODS

This outbreak investigation includes 12 patients from PICU between the ages of 2 months and 4 years (mean 16 months, 7 male). To identify the origin, samples from all possible sources throughout the hospital were collected and ran through DNA isolation and Pulse Field Gel Electrophoresis.

RESULTS

120 samples were collected during the outbreak. 31 samples (26%) were positive for S maltophilia. 30 S maltophilia isolates were analyzed, 10 different genotypes were identified. Clustering isolates were grouped into 3 different clusters (tolerance and optimization 1.0, cutoff 90%). The largest cluster was genotype 1, which included 19 isolates, those belong to patients' samples and a sample from a pull-out faucet inside the PICU. The Pull-out faucet was the origin of the bloodstream infection.

DISCUSSION

Pull-out faucets allow biofilm production, due its structure. Pulse Field Gel Electrophoresis identifies the transmission dynamics of the outbreak, with its high discriminatory power.

CONCLUSIONS

Water sources should be monitored on a regular basis. Pull-out faucets enable bacterial overgrowth; therefore, we recommend water surveillance during outbreak investigations.

Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic

The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, blaNDM and blaOXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.

Characterization and Antibacterial Potential of Iron Oxide Nanoparticles in Eradicating Uropathogenic E. coli

Proper management and control measurements are needed to stop the spread of highly pathogenic E. coli isolates that cause urinary tract infections (UTI) by developing new antibacterial agents to ensure the safety of public health. Therefore, the present investigations were used to achieve the synthesis of iron oxide nanoparticles (IONPs) via a simple coprecipitation method using ferric nitrates Fe (NO3)3 as the precursor and hydrazine solution as the precipitator and to explore the antibacterial activity against eradicating Uropathogenic Escherichia coli (E. coli). The synthesized IONPs were further studied using a UV-vis spectrophotometer, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), and scanning electron microscopic (SEM) analysis. The maximum surface plasmon resonance peak was observed as absorption at 320 nm in a colloidal solution to validate the synthesis of IONPs. The FT-IR analysis was used to identify different photoactive functional groups that were responsible for the reduction of Fe (NO3)3 to IONPs. The crystalline nature of synthesized IONPs was revealed by XRD patterns with an average particle size ranging as 29 nm. The SEM image was employed to recognize the irregular morphology of synthesized nanoparticles. Moreover, significant antibacterial activity was observed at 1 mg/mL stock solution but after (125, 250, and 500 μg/mL) dilution, the synthesized IONPs showed moderate activity and became inactive at lower concentrations. The morphological and biochemical tests were used to confirm the presence of E. coli in the samples. Furthermore, the minimum inhibitory concentration (MIC) and minimum bacterial concentration (MBC) were carried out to determine the inhibitory concentrations for the isolated bacteria. The isolated E. coli were also subjected to antibiotic sensitivity testing that showed high resistance to antibiotics such as penicillin and amoxicillin. Thus, the findings of this study were to use IONPs against antibiotic resistance that has been developed in an inappropriate way.

Detection of clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex and Klebsiella pneumoniae isolated from farmed freshwater fish

AIMS

The present study was aimed to detect clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex (CR-ECC), Klebsiella pneumoniae (CR-KP), and Serratia plymuthica (CR-SP) isolated from farmed freshwater fish.

METHODS AND RESULTS

Out of 243 spatially diverse freshwater fish samples analysed, 5.3% were contaminated with CR-ECC, 1.6% with CR-KP, and 0.4% with CR-SP. The CR-ECC was further identified as E. asburiae (38.5%), E. mori (23.1%), E. cloacae (15.4%), E. hormaechei (15.4%), and E. kobei (7.7%) by 16S rRNA gene sequencing. The CR-ECC were resistant to carbapenems and cefoxitin, whereas CR-KP and CR-SP were multi-drug resistant (MDR). The CR-ECC harboured the carbapenemase gene blaIMI alone or in combination with blaTEM, blaEBC, blaCIT, blaACC, and tet(E). Whereas, CR-KP harboured carbapenemase gene, blaNDM-5 along with blaOXA-48, blaSHV, blaOXA-1, blaCTX-M-15, tet(A), sul1, and qnrB. No carbapenemase-encoding genes were detected in CR-SP. The MLST analysis showed that CR-KP belonged to ST231 and ST1561 lineages, while CR-ECC did not show exact match with any reported STs. The plasmid replicons predominantly detected were IncF and IncI1. Broth mating assays of CR-KP and CR-ECC with recipient Escherichia coli J53 indicated that blaNDM-5 was transferable but not blaIMI.

CONCLUSION

This study highlights the low-level contamination of carbapenem-resistant Enterobacterales (CRE) harbouring clinically relevant carbapenemase-encoding genes in farmed freshwater fish from India. The CR-ECC of fish origin did not show the potential to spread carbapenem resistance.

Prevalence, molecular characterization of integrons and its associated gene cassettes in Klebsiella pneumoniae and K. oxytoca recovered from diverse environmental matrices

The high prevalence of infections arising from Klebsiella species is related to their ability to acquire and disseminate exogenous genes associated with mobile genetic elements such as integrons. We assessed the prevalence, diversity, and associated gene cassettes (GCs) of integrons in Klebsiella species. The isolates recovered from wastewater and hospital effluents, rivers, and animal droppings were identified using the conventional Polymerase Chain Reaction (PCR) with primers targeting the gryA, pehX, and 16S-23S genes. The antimicrobial resistance profile and the Extended-Spectrum and Metallo β-lactamases production were carried out using standard microbiological techniques. PCR, DNA sequencing analyses, and Restriction Fragment Length Polymorphism were used to characterize the integrons and their associated GCs. Furthermore, the genotypic relationships between the different isolated K. pneumoniae were determined using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR. About 98% (51/52) of the confirmed isolates harboured an integrase gene, with 80% intI1, while the remaining 20% concurrently harboured intI1 and intI2, with no intI3 observed. About 78% (40/51) of the bacterial strains were positive for a promoter, the P2R2, investigated, while 80% (41/51) harboured at least one of the qacEΔ1 and sul1. Three different GCs arrangements identified were aac(6')-Ib, aadA1-dfrA1, and dfrA1-sat2. At a similarity index of 60%, the ERIC-PCR fingerprints generated were categorized into nine clusters. Our study is the first to reveal the features of integrons in Klebsiella spp. recovered from environmental sources in the Eastern Cape Province, South Africa. We conclude that the organisms' sources are repositories of integrons harbouring various gene cassettes, which can be readily mobilized to other microorganisms in similar or varied niches.

Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments

Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.

The mobile gene cassette carrying tetracycline resistance genes in Aeromonas veronii strain Ah5S-24 isolated from catfish pond sediments shows similarity with a cassette found in other environmental and foodborne bacteria

Aeromonas veronii is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen that causes diarrhea in humans and hemorrhagic septicemia in fish. In the present study, we used whole-genome sequencing (WGS) to evaluate the presence of antimicrobial resistance (AMR) and virulence genes found in A. veronii Ah5S-24 isolated from catfish pond sediments in South-East, United States. We found cphA4, dfrA3, mcr-7.1, valF, blaFOX-7, and blaOXA-12 resistance genes encoded in the chromosome of A. veronii Ah5S-24. We also found the tetracycline tet(E) and tetR genes placed next to the IS5/IS1182 transposase, integrase, and hypothetical proteins that formed as a genetic structure or transposon designated as IS5/IS1182/hp/tet(E)/tetR/hp. BLAST analysis showed that a similar mobile gene cassette (MGC) existed in chromosomes of other bacteria species such as Vibrio parahaemolyticus isolated from retail fish at markets, Aeromonas caviae from human stool and Aeromonas media from a sewage bioreactor. In addition, the IS5/IS1182/hp/tet(E)/tetR/hp cassette was also found in the plasmid of Vibrio alginolyticus isolated from shrimp. As for virulence genes, we found the tap type IV pili (tapA and tapY), polar flagellae (flgA and flgN), lateral flagellae (ifgA and IfgL), and fimbriae (pefC and pefD) genes responsible for motility and adherence. We also found the hemolysin genes (hylII, hylA, and TSH), aerA toxin, biofilm formation, and quorum sensing (LuxS, mshA, and mshQ) genes. However, there were no MGCs encoding virulence genes found in A. veronii AhS5-24. Thus, our findings show that MGCs could play a vital role in the spread of AMR genes between chromosomes and plasmids among bacteria in aquatic environments. Overall, our findings are suggesting that MGCs encoding AMR genes could play a vital role in the spread of resistance acquired from high usage of antimicrobials in aquaculture to animals and humans.

Class 1 and 2 Integrons in Escherichia coli Strains Isolated from Diarrhea and Bacteremia in Children Less Than 2 Years of Age from Peru

Class 1 and Class 2 integrons are mobilizable elements able to carry a variety of antibiotic resistance determinants. In the present study, Class 1 and 2 integrons present in 355 pathogenic Escherichia coli (285 diarrheagenic, of these 129 were enteropathogenic, 90 enteroaggregative, 66 enterotoxigenic, and 70 bacteremic) isolated from healthy and ill children under age 5 from periurban areas of Lima, Peru, were characterized. The presence of integrase 1 and 2 was established by polymerase chain reaction (PCR), and variable regions were grouped by PCR-restriction fragment length polymorphism and subsequent sequencing. Antimicrobial resistance was established by disk diffusion. Ninety-seven isolates (27.3%) presented integrase 1, and 16 (4.5%) presented integrase 2 (P < 0.0001); in addition, seven (2.0%) isolates, six diarrheagenic and one bacteremic, presented both integrase genes. The presence of integrase 1 was more frequent among bacteremic isolates (P = 0.0004). Variable regions were amplified in 76/120 (63.3%) isolates with up to 14 gene arrangements. The most prevalent gene cassettes were those encoding dihydrofolate reductases as well as aminoglycoside modifying enzymes. Of note, Class 1 integrons tended to be associated with the presence of extended-spectrum β-lactamases (ESBLs). A variety of Class 1 and 2 integrons were detected in diarrheagenic and bacteremic E. coli, demonstrating the heterogeneity of variable regions circulating in the area. The association of integrons with ESBLs is worrisome and has an impact on the development of multidrug resistance.

Antimicrobial resistance and genetic diversity of Staphylococcus aureus collected from livestock, poultry and humans

Staphylococcus aureus is one of the most prominent nosocomial, community and farm acquired bacterial infections among animals and human populations. The main purpose of our study was to identify and characterize antimicrobial resistance (AMR) among Staphylococcus aureus isolated from livestock, poultry and humans and to further identify the associated genes. Staphylococcus aureus isolates from human, bovine, swine and poultry were collected from different laboratories across the United States collected between 2003 and 2016. Antimicrobial susceptibility testing for 13 antimicrobials was performed and conventional PCR was used to detect the presence of the nuc gene, mec gene, and to detect int1 gene. Associations between the presence of mec and intl and specific AMR profiles were determined. Antimicrobial resistance was detected in all four host categories, with the highest overall rates found in swine, 100% resistant to tetracycline, 88% to penicillin and 64% clindamycin. The next highest was found among humans with 81.6% of isolates resistant to penicillin followed by 44% to clindamycin and 43% to erythromycin. Among beef cattle isolates, 63.2% were resistant to penicillin, 15.8% resistant to clindamycin and 15.8% to erythromycin. No isolates from any of the hosts were resistant to linezolid. Among poultry isolates, the highest AMR was found to clindamycin, followed by erythromycin and penicillin. Among dairy cattle, highest resistance was found to penicillin, followed by chloramphenicol and gentamicin. Dairy cattle were the only host category with isolates that are resistant to trimethoprim-sulfamethoxazole. Of the 220 isolates detected by latex agglutination, 217 were confirmed to be S. aureus via PCR of the nuc gene, 21.4% were positive for the mecA gene. Swine had the highest prevalence of the mecA gene, followed by humans, poultry and beef cattle. This study has demonstrated a high occurrence of penicillin resistance among all S. aureus isolates. There were differences observed between host species with tetracycline resistance being the highest among swine isolates and clindamycin being highest in poultry isolates. No detection of oxacillin resistance was found in isolates from dairy cattle but was found in isolates from all of the other host species, 94% of which contained the mecA gene.

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High occurrence of penicillin resistance in Staphylococcus aureus isolates collected from livestock, poultry and humans.

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Tetracycline resistance was the highest among swine isolates and clindamycin was the highest in poultry isolates.

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Oxacillin resistance was not detected among dairy cattle isolates but was found in isolates from other host species.

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Ninety four percent of the S. aureus isolates were resistant to oxacillin contained the mecA gene.

Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables

Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and bla_TEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.

Genetic characterization of third- or fourth-generation cephalosporin-resistant avian pathogenic Escherichia coli isolated from broilers

The third- or fourth-generation cephalosporins (3GC or 4 GC) are classified as "critically important antimicrobials for human medicine" by WHO, but resistance to these drugs is increasing rapidly in avian pathogenic E. coli (APEC). This study investigated the distribution and genetic characteristics of 3GC- or 4 GC-resistant APEC isolates from five major integrated broiler operations in Korea. The prevalence of 3GC- or 4GC-resistant APEC isolates in 1-week-old broilers was the highest in farms of operation C (53.3%); however, the highest prevalence of these isolates in 4-week-old broilers was the highest on the farms of operation A (60.0%), followed by operations E (50.0%) and C (35.7%). All 49 3GC- or 4GC-resistant APEC isolates had at least one β-lactamase-encoding gene. The most common β-lactamase-encoding genes was extended-spectrum β-lactamase gene, bla CTX-M-15, detected in 24 isolates (49.0%), followed by bla TEM-1 (32.7%). Sixteen isolates (32.7%) harbored class 1 integrons, and four isolates (8.2%) showed different gene cassette-arrangements. However, only 1 of 26 isolates harboring class 2 integrons carried a gene cassette. Furthermore, both CRISPR 1 and 2 arrays were detected in most isolates (36 isolates; 73.5%), followed by CRISPR 2 (18.4%) and CRISPR 1 (4.1%). Interestingly, CRISPR 2 was significantly more prevalent in multidrug resistant (MDR)-APEC isolates than in non-MDR APEC isolates, whereas CRISPR 3 and 4 were significantly more prevalent in non-MDR APEC isolates (each 11.1%; p < 0.05). None of the protospacers of CRISPR arrays were directly associated with antimicrobial resistance. Our findings indicate that the distribution and characteristics of 3GC or 4GC-resistant APEC isolates differed among the integrated broiler operations; moreover, improved management protocols are needed to control the horizontal transmission of 3GC or 4GC-resistant APEC isolates.

Temperature affects variations of class 1 integron during sludge anaerobic digestion

Revealing class 1 integron characteristics under different operating conditions is of great importance to control antibiotic resistance genes (ARGs) during sludge anaerobic digestion (AD). This study investigated the variations of class 1 integrons and the ARGs carried by class 1 integrons in anaerobic sludge digesters under 25 °C, 35 °C, and 55 °C. The results showed lower intI1 abundance and fewer class I integrons with long gene cassette arrays at 55 °C than at 25 °C and 35 °C. Multi-resistance gene cassette arrays were observed in the digesters at 25 °C and 35 °C. Abundant ARGs were detected on class 1 integrons in all digesters with aminoglycosides as the dominant class. The abundance of ARGs on class 1 integrons in digesters at 55 °C was lower than that at 25 °C and 35 °C. Thermophilic AD is better than mesophilic ones in the control of ARGs carried by class 1 integrons.

The large plasmid carried class 1 integrons mediated multidrug resistance of foodborne Salmonella Indiana

Salmonella enterica serovar Indiana (S. Indiana) has aroused widespread concern as an important zoonotic pathogen. The molecular mechanism of multidrug resistance (MDR) in S. Indiana is not known and should be assessed. We aim to investigate the molecular mechanism of MDR and the importance of large plasmids carried class 1 integrons in the MDR of foodborne S. Indiana. Class 1 integrons in 48 S. Indiana isolates and 200 isolates of 7 other Salmonella serotypes were detected by polymerase chain reaction (PCR). To analyze the antimicrobial resistance genes (ARGs) of two S. Indiana isolates, designated S. Indiana 15 and S. Indiana 222, next-generation sequencing (NGS) was performed, and the resulting sequences were compared with the complete nucleotide sequences of S. Indiana D90 and S. Indiana C629. Comparative functional analysis was conducted between the intI1 (1,014 bp) of S. Indiana 222 and the intI1 (699 bp) of S. Indiana 15. Plasmid conjugation transfer analysis was performed to analyze the horizontal gene transfer of the integrons-related resistance genes with integron-positive and integron-negative Salmonella isolates. 64.58% of S. Indiana isolates carried class 1 integrons, which was significantly higher than that of other Salmonella serotypes (p < 0.001). The NGS results showed that the S. Indiana 15 and S. Indiana 222 isolates carried a large plasmid with a class 1 integron and multiple ARGs, similar to S. Indiana D90 and S. Indiana C629. Two integrases found in S. Indiana isolates belong to class 1 integrases and could integrate resistance genes into specific integration sites of the integrons. The conjugation frequency of intI1 (1,014 bp) was 6.08 × 10⁻⁵, which was significantly higher than that of intI1 (699 bp) (p < 0.01). The large plasmids carrying a class 1 integron and the number of ARGs were strongly correlated (p < 0.001). The conjugation frequency of integron-positive S. Indiana recipient isolates was significantly higher than that of integron-negative recipient isolates (p < 0.05). S. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones.

Graphical abstract

Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens

Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.

Multi-Drug Resistance to Salmonella spp. When Isolated from Raw Meat Products

Salmonella spp. is the most frequent cause of foodborne diseases, and the increasing occurrence of MDR strains is an additional and increasing problem. We collected Salmonella spp. strains isolated from meat (poultry and pork) and analysed their antibiotic susceptibility profiles and the occurrence of resistance genes. To determine the susceptibility profiles and identify MDR strains, we used two MIC methods (MICRONAUT and VITEC2 Compact) and 25 antibiotics. Phenotypic tests showed that 53.84% strains were MDR. Finally, molecular analysis strains revealed the presence of blaSHV, blaPSE-1, blaTEM, but not blaCTX-M genes. Moreover, several genes were associated with resistance to aminoglycosides, cephalosporins, fluorochinolones, sulfonamides, and tetracyclines. This suggests that further research on the prevalence of antibiotic resistance genes (ARGs) in foodborne strains is needed, especially from a One Health perspective.

Shiga toxin-producing Escherichia coli O157 in piglets and food from backyard systems

Piglets suffer from diarrhea caused by the Shiga toxin-producing Escherichia coli (STEC) and can be carriers of the bacteria, with public health consequences in developing countries. The aim of the present study was to study the prevalence of STEC O157 in feces of 465 piglets and 54 food mixes from backyard systems, the antimicrobial susceptibility of STEC and the frequency of genes encoding extended-spectrum β-lactamases. The E. coli was isolated from 75.90 % of the evaluated feces. The STEC strains were identified in 33.11% of the sampled population and in 43.60% of the piglets carrying E. coli. Among STEC strains, the stx1 gene was the most frequent (22.30%). The rfbO157 gene was amplified in 47.40% of the STEC strains. High frequencies of STEC strains were not susceptible to ampicillin, carbenicillin and tetracycline. The blaTEM gene (52) was the most frequent among strains not susceptible to ampicillin. Class 1 integrons were the most frequent in those strains. Of the identified STEC strains, 48.70% were considered as multi-drug resistant and 1.90% were considered extensively drug resistant. In the supplied food, STEC O157 strains were identified in 25.00% of the STEC strains. We conclude that the piglets from backyard systems are carriers of STEC O157 strains not susceptible to common antibiotics, including penicillins and tetracyclines. In addition, supplied food is a source of this type of pathogenic bacteria. Through their direct contact with humans, the piglets and food represent a potential source of bacterial dissemination capable of producing gastrointestinal infections in humans.

Prevalence and characterisation of antimicrobial resistance genes and class 1 and 2 integrons in multiresistant Escherichia coli isolated from poultry production

A global increase in the populations of drug resistant bacteria exerts negative effects on animal production and human health. Our study has been focused on the assessment of resistance determinants in relation to phenotypic resistance of the 74 commensal E. coli isolates present in different ecological environments. The samples were collected from poultry litter, feces, and neck skin. Among the microorganisms isolated from the poultry litter (group A), the highest resistance was noted against AMP and DOX (100%). In the E. coli extracts from the cloacal swabs (group B), the highest resistance was observed against AMP (100%) and CIP (92%). The meat samples (group C) were characterized by resistance to AMP (100%) and STX (94.7%). Genes encoding resistance to β-lactams (bla_TEM, bla_CTX-M), fluoroquinolones (qnrA, qnrB, qnrS), aminoglycosides (strA-strB, aphA1, aac(3)-II), sulfonamides (sul1, sul2, sul3), trimethoprim (dfr1, dfr5, dfr7/17) and tetracyclines (tetA, tetB) were detected in the studied bacterial isolates. The presence of class 1 and 2 integrons was confirmed in 75% of the MDR E. coli isolates (plasmid DNA), of which 60% contained class 1 integrons, 15% contained class 2 integrons, and 11.7% carried integrons of both classes. Thus, it may be concluded that integrons are the common mediators of antimicrobial resistance among commensal multidrug resistant Escherichia coli at important stages of poultry production.

Incidence and Molecular Characterization of Carbapenemase Genes in Association with Multidrug-Resistant Clinical Isolates of Pseudomonas aeruginosa from Tertiary Healthcare Facilities in Southwest Nigeria

Pseudomonas aeruginosa, resistant to multiple antibacterial agents including carbapenems, is of great global public health concern. There is limited data available regarding incidence of Metallo-Beta Lactamase producing P. aeruginosa, their molecular basis of resistance in particular carbapenem resistance and any genetic relatedness among circulating clinical isolates in Southwest Nigeria. Four hundred and thirty P. aeruginosa isolates were collected from seven tertiary care hospitals (predominantly from wound, ear, and urinary tract infections) and verified by PCR targeting oprI and oprL. Antibiotic susceptibility using 16 selected antibiotics and MBL screening was performed. The integrons (class 1, 2 and 3) and carbapenemase genes- bla_GES, bla_NMC-A, bla_BIC-1, bla_SME, bla_IMP, bla_VIM, bla_SPM, bla_NDM, bla_AIM, bla_DIM, bla_SIM, bla_GIM, bla_OXA-48, bla_OXA-58 were detected by PCR and were sequenced. Quantitative real-time polymerase chain reaction was used to quantify expression levels of eight efflux pump genes, ampC cephalosporinase and outer membrane porin, oprD. The isolates were genotyped using Enterobacterial Repetitive Intergenic Consensus sequence Polymerase Chain Reaction (ERIC-PCR). Four hundred and thirty P. aeruginosa isolates were subjected to antibiotic susceptibility testing, revealing that 109 (25.4%) isolates were multidrug-resistant, 47 (10.9%) were extensively drug-resistant and 25 (5.8%) were pandrug-resistant. MBL was seen in 17.0% (73/430) isolates. MBL-encoding genes; bla_VIM-5 and bla_NDM-1 were detected in 86.3% (63/73) isolates, with bla_VIM-5 and bla_NDM-1 in 35.6% (26/73) and 38.4% (28/73), respectively, whereas co-occurrence of bla_VIM-5 and bla_NDM-1 was found in 12.3% (9/73). Forty-one (56.2%) carbapenem-resistant P. aeruginosa strains carried class 1 integrons, while co-occurrence of class 1 and 2 integrons was seen in 12.3%. qPCR results indicated that MexXY-OprM was highly expressed pump in 58.9%, ampC upregulated in 26.0%, while oprD porin was downregulated in 65.8% isolates. ERIC-PCR results suggest that carbapenem-resistant strains exhibit genetic heterogeneity. The high incidence of MBL-encoding genes and integrons in diversified clinical P. aeruginosa from southwestern Nigeria is of great concern. The co-occurrence of bla_VIM-5 and bla_NDM-1 as well as resistance in general manifesting a gradient based on genotypic variation suggests that there is a strong need for efficient surveillance programs and antibiotic stewardship.

Identification and characterization of class 1 integrons among multidrug-resistant uropathogenic Escherichia coli strains in Mexico

This study aimed to identify and characterize integrons among multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) from outpatients in Mexico City, Mexico. PCR assays were used to screen for the presence of class 1, 2 and 3 integrons, whose PCR products were sequenced to identify the inserted gene cassettes within the variable regions. Out of 83 tested strains, 53 (63.9%) were positive for the presence of class 1 integrons, whereas no integrons were detected in the remaining strains, regardless of their classes. Most of the strains carrying the intI1 gene belonged to the extraintestinal B2 (41.5%) and commensal A (32.1%) phylogroups, and to a lesser extent, the extraintestinal D (20.8%) and commensal B1 (5.7%) phylogroups. Moreover, 8 different gene cassette arrangements were detected, with dfrA17 and aadA5 being the most common (32.1% of the class 1 integron-positive strains), which confer resistance to trimethoprim/sulfamethoxazole and aminoglycosides, respectively. Our results suggest that class 1 integrons are widely distributed among MDR-UPEC strains in Mexico, which may directly or indirectly contribute to the selection of MDR strains. These findings are important for a better understanding of the factors and mechanisms that promote multidrug resistance among UPEC strains.

Antimicrobial resistance in Indian isolates of non typhoidal Salmonella of livestock, poultry and environmental origin from 1990 to 2017

A retrospective antimicrobial resistance study of nontyphoidal Salmonella enterica isolates from India during 1990-2017 was conducted to study the microbial susceptibility to antibiotics. A total of 271 Salmonella enterica isolates from poultry (n = 146), farm animals (n = 55) and environmental sources (n = 70) were tested for susceptibility using 15 antimicrobial drugs. The drug classes include aminoglycosides, phenicols, cephalosporins, penicillins, carbapenems, fluoroquinolones, and sulphonamide-trimethoprim. Study revealed that overall, 133 (49.08%) of 271 isolates were resistant to ≥ 1 antimicrobial drugs and 81 (29.89%) out of 271 isolates were multidrug resistant (resistance to ≥ 3 drugs). Majority (68.96%) of Typhimurium serovars (n = 87) were susceptible to all antibiotics tested, whereas only 5% Kentucky serovars (n = 40) were pan susceptible. All the drugs revealed decreasing trend of susceptibility from 1990 towards 2017 except cephalosporins and carbapenems. Statistical analysis of association between time period and antimicrobial resistance revealed a significance of < 0.05. Molecular detection of genetic determinants associated with antimicrobial resistance revealed the presence of genes like class I integrons, sul1, sul2, catIII, cmlA, dfrA, bla_TEM, bla_AmpC in the resistant isolates. Furthermore, plasmid mediated quinolone resistant determinants like qnrD and qnrS were also reported in the current study.

Molecular Characterization of Class 1, 2 and 3 Integrons in Serratia spp. Clinical Isolates in Poland - Isolation of a New Plasmid and Identification of a Gene for a Novel Fusion Protein

Purpose

Gram-negative rods of the genus Serratia play an increasing role as etiological agents of healthcare-associated infections (HAI) in humans. These bacteria are characterized by natural and acquired resistance to several groups of antibacterial agents. The aim of the study was to characterize class 1, 2 and 3 integrons in the clinical isolates of Serratia spp. in Poland.

Methods

The study comprised 112 clinical strains of Serratia, isolated from patients hospitalized in Poland in 2010-2012. Identification of strains was confirmed using MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) system. Detection of class 1, 2 and 3 integrase DNA sequence was performed by multiplex-PCR. Amplicons obtained in the PCR reactions were purified and then sequenced bidirectionally.

Results

Among the analyzed strains, Serratia marcescens was a predominant species (103/112, 92.0%). All three classes of integrase DNA sequence were detected in the analyzed strains of Serratia spp. DNA sequence of class 3 integron, besides integrase gene, revealed three gene cassettes (dfrB3, bla _GES-7,bla _{OXA/aac(6')-Ib-cr}). BLAST analysis of DNA sequence revealed that class 3 integron was carried on 9448 bp plasmid which was named pPCMI3 - whole sequence of its DNA was submitted to GenBank NCBI (National Center for Biotechnology Information) - NCBI MH569711.

Conclusion

In this study, we identified a new plasmid pPCMI3 harboring class 3 integron. This is the first report of a gene oxa/aac(6')-Ib-cr coding for a novel fusion protein, which consists of OXA β-lactamase and acetyltransferase aac(6')-Ib-cr. In the analyzed strains, class 1 and 2 integrons were also detected. Among the strains with class 1 integron, nine contained cassette array 5'CS-aadA2-ORF-dfrA12-3'CS, and two - cassette array 5'CS-aacC1-ORF-ORF-aadA1-3'CS, which were not previously reported in Serratia spp.

Characterization and Antimicrobial Resistance of Environmental and Clinical Aeromonas Species Isolated from Fresh Water Ornamental Fish and Associated Farming Environment in Sri Lanka

The aims of this study were to characterize and investigate antimicrobial susceptibility and presence of integrons in 161 Aeromonas spp. isolated from ornamental freshwater fish farming environment, apparently healthy and diseased fish. Phylogenetic analyses of the gyrB gene sequences identified Aeromonas veronii as the most abundant species (75.8%) followed by Aeromonashydrophila (9.3%), Aeromonas caviae (5%), Aeromonas jandaei (4.3%), Aeromonas dhakensis (3.7%), Aeromonas sobria (0.6%), Aeromonas media (0.6%), and Aeromonas popoffii (0.6%). Susceptibility to thirteen antimicrobials was determined and antimicrobial resistance frequencies were: amoxicillin (92.5%), enrofloxacin (67.1%), nalidixic acid (63.4%), erythromycin (26.1%), tetracycline (23.6%), imipenem (18%), trimethoprim-sulfamethoxazole (16.8%), and gentamicin (16.8%). Multi-drug resistance (MDR) was widespread among the isolates (51.6%, 83/161) with 51.6% (63/122) A. veronii isolates being MDR. In addition, 68.3% of isolates had multiple antibiotic resistance (MAR) indexes higher than 0.2, suggesting that they originated from a high-risk source of contamination where antimicrobials are often used. In all, 21.7% isolates carried class 1 integrons, with 97.1% having gene cassettes, while there were 12 isolates carrying class 2 integron gene cassettes. Our findings highlight that the aquatic environment and ornamental fish act as reservoirs of multidrug resistant Aeromonas spp. and underline the need for a judicious use of antimicrobials and timely surveillance of antimicrobial resistance (AMR) in aquaculture.

High incidence of multi-drug resistance and heterogeneity of mobile genetic elements in Escherichia coli isolates from diseased ducks in Sichuan province of China

Harmonious ecological environment is a major concern with rising feeding and consumption of ducks, as these waterfowl birds can promote the spread of antibiotic resistant genes (ARGs). Therefore, this study was conducted to know diversity of antimicrobial resistance (AMR), integrons, and mobile genetic elements (MGEs) in Escherichia coli (E. coli) isolated from intestinal contents or pericardial effusion of diseased ducks from 2018 to 2020 in Sichuan, China. The AMR phenotype was determined via disk diffusion test in 165 E. coli isolates. Further, the integrase genes of integron (intI1, intI2 and intI3 genes), gene cassettes (GCs) and MGEs were screened by PCR and sequencing. The results indicated 100% isolates were resistant to at least one antibiotic and 98.8% were multidrug-resistant strains. Highest AMR phenotype was recorded to rifampin (97.0%) followed by ampicillin (95.8%), chloramphenicol (89.7%), trimethoprim-sulfamethoxazole (84.2%), ciprofloxacin (83.0%), cefotaxime (80.0%), streptomycin (75.8%), doxycycline (49.7%), amikacin (10.3%), amoxicillin/clavulanic acid (3.6%), polymyxin B (1.2%) and ertapenem (0.6%). Further, class 1 and 2 integrons were found in 87.3% and 17.6% isolates, respectively. All isolates were negative for intI3 gene. The variable region of class 1 and 2 integrons contained total 13 different GCs, including arr-3+dfrA27, dfrA1+aadA1, dfrA17+aadA5, dfrA12, dfrA1+sat2+aadA1, dfrA12+aadA2, dfrA5, aadA2+ere(A)+dfrA32, aac(6')-Ib-cr, aadA22, aadA5, dfrA17, and dfrA27. Moreover, 13 MGEs in 69 different combinations were observed with predominance of IS26 followed by tnpA/Tn21, trbC, ISEcp1, merA, ISAba1, tnsA, tnsB, tnsC, IS1133, tnsD, ISCR3/14, and tnsE. Thus, the monitoring of integrons, MGEs and ARGs is important to understand the complex mechanism of AMR, which might help to introduce interventions for prevention and control of AMR in duck farms in China.

Determination and molecular analysis of antibiotic resistance in Gram-negative enteric bacteria isolated from Pelophylax sp. in the Eastern Black Sea Region

The aim of this study was to evaluate the prevalence and types of antimicrobial resistance among Gram-negative enteric bacteria isolated from Pelophylax sp. Fifty-four frogs were collected from six provinces in the Eastern Black Sea Region of Turkey. In the cloacal swab cultures, bacteria from 160 different colonies were identified by biochemical tests, automated systems, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry. The antimicrobial susceptibility tests were performed by the disk diffusion method. The observed drug resistance rate was the highest to ampicillin and cefazolin, while the lowest against ciprofloxacin and tetracycline. In the molecular assays, bla TEM (8 Citrobacter spp.), bla SHV (2 Escherichia coli, 1 Hafnia alvei, and a Serratia liquefaciens), tetA genes (E. coli and Klebsiella spp.) and a class 1 integron without any gene cassette (E. coli) were detected. Among the strains, no plasmid-mediated quinolone resistance [qnrA, qnrB, qnrS, qepA and aac (6 ')-Ib-cr] was found. However, two of three quinolone-resistant Klebsiella strains showed the novel amino acid substitution in the gyrA gene resulting in Ser83Asp and Asp87Glu.The clonality between E. coli isolates was also examined by pulsed-field gel electrophoresis. We consider that multidrug-resistant Gram-negative enteric bacteria in the intestinal microbiota of a cosmopolitan frog species might be a reservoir for antibiotic resistance genes.

Investigation of class 1 integrons and virulence genes in the emergent Salmonella serovar Infantis in Turkey

The emerging situation of Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) in Turkey was investigated in terms of virulence genes and mobile genetic elements such as Salmonella genomic island 1 (SGI1) and class 1 (C1) integron to see whether increased multidrug resistance (MDR) and ability to cause human cases is a consequence of their possession. Screening of SGI1 (and its variants) and C1 integrons was done with conventional PCR, while screening of gene cassettes and virulence genes was conducted with real-time PCR for 70 S. Infantis isolates from poultry products. SGI1 or its variants were not detected in any of the isolates. Sixty-eight of 70 isolates were detected to carry one C1 integron of size 1.0 kb. These integrons were detected to carry ant(3″)-Ia gene cassette explaining the streptomycin/spectinomycin resistance. Sequence analysis of gene cassettes belongs to four representing isolates which showed that, although their difference in isolation date and place, genetically, they are 99.9% similar. Virulence gene screening was introduced as genotypic virulence profiles. The most dominant profile for S. Infantis isolates, among twelve genes, was gatC-tcfA, which are known to be related to colonization at specific hosts. This study revealed the high percentage of C1 integron possession in S. Infantis isolates from poultry products in Turkey. It also showed the potential of S. Infantis strains to be resistant to more antimicrobial drugs. Moreover, a dominant profile of virulence genes that are uncommon for non-typhoidal Salmonella (NTS) serovars was detected, which might explain the enhanced growth at specified hosts.

From the Urinary Catheter to the Prevalence of Three Classes of Integrons, β-Lactamase Genes, and Differences in Antimicrobial Susceptibility of Proteus mirabilis and Clonal Relatedness with Rep-PCR

Introduction

Proteus mirabilis is a biofilm-forming agent that quickly settles on the urinary catheters and causing catheter-associated urinary tract infections. Thus, the spread of multidrug-resistant P. mirabilis isolates, with the ability to form a biofilm that carries integron, extended-spectrum β-lactamases (ESBLs), and plasmid-mediated colistin resistance genes (mcr), represents a severe threat to managing nosocomial infectious diseases. This study is aimed at surveying the prevalence of ESBL, integrase, and mcr genes of P. mirabilis, isolated from the catheter, to assess the differences in their antimicrobial susceptibility and clonal dissemination.

Method

Microtiter plate assay was adopted to measure biofilm formation. The antimicrobial susceptibility was assessed by the disk diffusion method. Antimicrobial resistance genes (intI1, intI2, intI3, bla_TEM, bla_CTX-M, bla_SHV, mcr1, and mcr2) were detected by PCR. All of the isolates were characterized by repetitive sequence-based PCR.

Result

From 385 collected catheters in patients admitted to the intensive care unit (ICU), 40 P. mirabilis were isolated. All of the isolates could form a biofilm. Proteus spp. had intrinsic resistance to tetracycline (95%) and nitrofurantoin (92.5%), which explains the high resistance prevalence. The most widely resistant antibiotic was trimethoprim-sulfamethoxazole (75%). Thirty-three (82.5%) isolates were classified as multidrug resistance (MDR). The prevalence of intI1 and intI2 genes was 60% and 25%, respectively. In 6 (15%) isolates, both genes were detected. The most frequent ESBL gene detected in all of the isolates was bla_TEM. Also, no detection for mcr1 and mcr2 antibiotic resistance genes was reported. Rep-PCR identified 39(GTG)5 types (G1–G39) of 40 isolates that 38 isolates had unique patterns.

Conclusion

In this study, 82.5% of isolates were MDR with high antibiotic resistance to trimethoprim-sulfamethoxazole. The intI1 and bla_TEM were the most prevalent genes in the integrase and ESBL gene family. High diversity was seen in the isolates with Rep-PCR. The increasing rate of MDR isolates with a high prevalence of resistance genes could be alarming and demonstrate the need for hygienic procedures to prevent the increased antibiotic resistance rate in the future.

Antibiotic Resistance Profile of Salmonella enterica Isolated from Exotic and Indigenous Leafy Green Vegetables in Accra, Ghana

ABSTRACT

Fresh produce-borne enteric bacterial pathogens that are resistant to antibiotics have posed serious challenges to food safety and public health worldwide. This study was conducted to evaluate the antibiotic resistance profiles of Salmonella enterica isolates (n = 33) recovered from exotic and indigenous leafy green vegetable samples (n = 328) collected from 50 vegetable farms in 12 farming areas and 37 vegetable sellers in four market centers in Accra, Ghana, from March 2016 to March 2017 and to determine the distribution of integrons among antibiotic-resistant isolates. The susceptibility of the Salmonella isolates to 12 antibiotics was assayed with the standard disk diffusion assay. The MICs of the five most resisted antibiotics were determined with a twofold macrodilution method. A PCR assay was used to detect the presence of integrons in Salmonella isolates, and PCR products with the amplified integron gene cassette were purified and sequenced with the Sanger sequencing technology. The Salmonella isolates used in the study were resistant to at least one tested antibiotic, and 30.3% (10 of 33) of the isolates were multidrug resistant. Most isolates (81.8%) were resistant to sulfisoxazole. The MICs of tetracycline, cefoxitin, streptomycin, ampicillin, and sulfisoxazole were 16, 32, 64, 64, and >1,024 μg/mL, respectively. Five patterns of multidrug resistance were observed among the Salmonella isolates, and the most common patterns were AAuFox (30.3%) and AAuFoxSSu (18.1%). One (3.0%) of the 33 Salmonella isolates tested positive for the class 1 integron, with a gene cassette of about 800 bp. Nucleotide sequencing revealed that this class 1 integron carried a single gene, dfrA7. Further studies are needed to determine whether the consumption of contaminated leafy green vegetables is a route for acquiring antibiotic-resistant Salmonella in Accra, Ghana.

HIGHLIGHTS

Antibiotyping and genotyping of extensively drug-resistant (XDR) Salmonella sp. isolated from clinical samples of Lahore, Pakistan

AIMS

Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi. The objective of this study was to evaluate the prevalence of XDR Salmonella among local population of Lahore and genotyping of isolates for antibiotic-resistant genes.

METHODS AND RESULTS

A total of 200 blood samples from suspected typhoid fever patients were collected. One hundred and fifty-seven bacterial samples were confirmed as Salmonella Typhi and 23 samples were confirmed as Salmonella Paratyphi after biochemical, serological and PCR based molecular characterization. Antibiogram analysis classified 121 (67·2%) Salmonella isolates as MDR and 62 isolates (34·4%) as XDR. The predominant resistance gene was ampC with 47·7% prevalence, followed by gyrA, catA1, tet(A), aac (3)-la, qnrS, bla_NDM-1 and bla_CTX-M-15 genes in 45·5, 40, 21·6, 18·3, 11·6, 2·2 and 0·5% isolates respectively. Sequence analysis showed the presence of sul1 and dfrA7 gene cassette arrays in 12 class 1 integron integrase positive isolates.

CONCLUSION

Large number of clinical XDR S. Typhi-resistant against third generation cephalosporins have been reported.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current study highlights the possible emergence of clinical XDR S. Typhi cases in Lahore, Pakistan. Potential attribution of phenotypic and genotypic XDR cases may help to contribute targeted therapy.

Identification and characterization of two novel ISCR1-associated genes dfrA42 and dfrA43 encoding trimethoprim resistant dihydrofolate reductases

Two novel ISCR1-associated dfr genes, dfrA42 and dfrA43, were identified from trimethoprim (TMP)-resistant Proteus strains and were shown to confer high level TMP resistance (MIC ≥ 1024 mg/L) when cloned into Escherichia coli These genes were hosted by complex class 1 integrons suggesting their potentials for dissemination. Analysis of enzymatic parameters and TMP affinity were performed, suggesting that the mechanism of TMP resistance for these novel DHFRs is the reduction of binding with TMP.

Genetic Characterization of AmpC and Extended-Spectrum Beta-Lactamase Phenotypes in Escherichia coli and Salmonella From Alberta Broiler Chickens

Horizontal gene transfer is an important mechanism which facilitates bacterial populations in overcoming antimicrobial treatment. In this study, a total of 120 Escherichia coli and 62 Salmonella enterica subsp. enterica isolates were isolated from broiler chicken farms in Alberta. Fourteen serovars were identified among Salmonella isolates. Thirty one percent of E. coli isolates (37/120) were multiclass drug resistant (resistant to ≥ 3 drug classes), while only about 16% of Salmonella isolates (10/62) were multiclass drug resistant. Among those, eight E. coli isolates had an AmpC-type phenotype, and one Salmonella isolate had an extended-spectrum beta-lactamase (ESBL)-type beta-lactamase phenotype. We identified both AmpC-type (bla_CMY-2) and ESBL-type (bla_TEM) genes in both E. coli and Salmonella isolates. Plasmids from eight of nine E. coli and Salmonella isolates were transferred to recipient strain E. coli J53 through conjugation. Transferable plasmids in the eight E. coli and Salmonella isolates were also transferred into a lab-made sodium azide-resistant Salmonella recipient through conjugation. The class 1 integrase gene, int1, was detected on plasmids from two E. coli isolates. Further investigation of class 1 integron cassette regions revealed the presence of an aadA gene encoding streptomycin 3’’-adenylyltransferase, an aadA1a/aadA2 gene encoding aminoglycoside 3’’-O-adenyltransferase, and a putative adenylyltransferase gene. This study provides some insight into potential horizontal gene transfer events of antimicrobial resistance genes between E. coli and Salmonella in broiler chicken production.

High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of bla_CTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, bla_TEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), bla_CTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where bla_CTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of bla_CTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of bla_CTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.

Integron mediated antimicrobial resistance in diarrheagenic Escherichia coli in children: in vitro and in silico analysis

The exchange of genes between bacterial chromosome and plasmid(s) and their integration into integrons are mainly responsible for acquisition and dissemination of antibiotic resistance. We investigated the role of integrons and their underlying molecular mechanisms leading to development of adaptability in E. coli and eventual resistance to antimicrobials. Escherichia coli isolates (n = 120); including 40 diarrheagenic isolates, an even number of isolates from cases other than diarrhea, and equal number of isolates from healthy children recovered from fresh stool samples were used for identification of integron genes and gene cassettes. The association of integrons with antibiotic resistance was assayed before phylogenetic analysis. DNA sequence analysis revealed class 1 and 2 integrons in 55.83% and 21.66% isolates, respectively. The integron presence was found significantly associated with the probability of antibiotic resistance in E. coli; the association being highest with class 1 integron. Modelling and molecular docking along with molecular dynamics simulation analyses found ceftriaxone and amoxicillin as potential inhibitors of dihydrofolate reductase (DHFR). The class 1 integrons of these pathogenic isolates can serve as prospective therapeutic targets using specific silencing strategies and combinational antimicrobial therapy. The findings may be useful for the development of a potent and versatile drug for DHFR inhibition.

Paper currency harbours antibiotic-resistant coliform bacteria and integron integrase

AIMS

This study was designed to analyse the prevalence of class 1 and class 2 integron integrase genes among antibiotic-resistant coliform bacteria isolated from paper currency circulating in Pakistan.

METHODS AND RESULTS

A total of 500 individual currency notes were collected from different food vending sites at Lahore, Pakistan. Bacterial population were identified by biochemical and PCR techniques. Antimicrobial susceptibility testing was performed by disc diffusion assay. The highest bacterial population on currency was found from street vendors and butcher shops. Escherichia coli was found to be the most prevalent coliform bacteria followed by Klebsiella sp. and Enterobacter sp. PCR amplification of antimicrobial resistance gene showed the presence of ampC, bla_TEM , bla_NDM-1 , qnrA, tet(A) and tet(B) genes among coliform isolates. A total of 47 integron integrase bearing strains of coliform bacteria were analysed. Sequence analysis showed the presence of dfrA1-aadA1, dfrA1, dfrA5, dfrA7, aadA1, aadA4 cassette arrays in class 1 integron and dfrA1-sat2-aadA1 in class 2 integrase genes.

CONCLUSION

Circulating currency was heavily contaminated with antimicrobial-resistant coliform bacteria bearing class 1 and class 2 integron integrase genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes a potential threat of severe bacterial infections due to improper hand hygiene and community sanitation when dealing with the currency notes.

Molecular characterization of antimicrobial resistance and enterobacterial repetitive intergenic consensus-PCR as a molecular typing tool for Salmonella spp. isolated from poultry and humans

Background and Aim:

Salmonella spp. are one of the most important food-borne pathogens in the world, emerging as a major public health concern. Moreover, multidrug-resistant (MDR) strains have been isolated from salmonellosis outbreaks, which compromise its treatment success. This study was conducted to characterize the phenotypic and genotypic antibiotic resistance profile of Salmonella strains isolated from broilers and humans from the regions of Tolima and Santander (Colombia).

Materials and Methods:

Salmonella spp. strains (n=49) were confirmed through molecular detection by amplification of the invA gene. Phenotypic antibiotic resistance was determined by the automated method and the agar diffusion method, and the presence of resistance genes was evaluated by PCR. Genotypic characterization was conducted using the enterobacterial repetitive intergenic consensus (ERIC)-PCR method, from which a dendrogram was generated and the possible phylogenetic relationships were established.

Results:

Salmonella isolates were classified as MDR strains exhibiting resistance to four antibiotic classes, penicillins, aminoglycosides, sulfonamides, and cephalosporins, and the human strains were resistant to gentamicin. At the genotypic level, the isolates contained the genes bla_CMY2, bla_CTX-M, bla_PSE-1, bla_TEM, aadA1, srtB, dfrA1, sul2, and floR. The genotyping results obtained by ERIC-PCR allowed the grouping of strains according to the source of isolation.

Conclusion:

The Salmonella spp. strains exhibited resistance to multiple antibiotics, as well as multiple genes associated with them, and the ERIC-PCR method was a technique that was helpful in generating clusters with biological significance.

Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study

The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.

Unravelling the menace: detection of antimicrobial resistance in aquaculture

One of the major problems to be addressed in aquaculture is the prominence of antimicrobial resistance (AMR). The occurrence of bacterial infections in cultured fishes promotes the continuous use of antibiotics in aquaculture, which results in the selection of proliferated antibiotic-resistant bacteria and increases the possibility of transfer to the whole environment through horizontal gene transfer. Hence, the accurate cultivation-dependent and cultivation-independent detection methods are very much crucial for the immediate and proper management of this menace. Antimicrobial resistance determinants carrying mobile genetic transfer elements such as transposons, plasmids, integrons and gene cassettes need to be specifically analysed through molecular detection techniques. The susceptibility of microbes to antibiotics should be tested at regular intervals along with various biochemical assays and conjugation studies so as to determine the extent of spread of AMR. Advanced omic-based and bioinformatic tools can also be incorporated for understanding of genetic diversity. The present review focuses on different detection methods to unearth the complexity of AMR in aquaculture. This monitoring helps the authorities to curb the use of antibiotics, commencement of appropriate management measures and adequate substitute strategies in aquaculture. The long battle of AMR could be overcome by the sincere implementation of One Health approach. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of antibiotics and increased antimicrobial resistance (AMR) are of major concerns in aquaculture industry. This could result in global health risks through direct consumption of cultured fishes and dissemination of AMR to natural environment through horizontal gene transfer. Hence, timely detection of the antimicrobial-resistant pathogens and continuous monitoring programmes are inevitable. Advanced microbiological, molecular biological and omic-based tools can unravel the menace to a great extent. This will help the authorities to curb the use of antibiotics and implement appropriate management measures to overcome the threat.

Genetic analysis and plasmid-mediated blaCMY-2 in Salmonella and Shigella and the Ceftriaxone Susceptibility regulated by the ISEcp-1 tnpA-blaCMY-2-blc-sugE

BACKGROUND

Nontyphoid Salmonella and Shigella can cause gastroenteritis in humans. Ceftriaxone (CRO) has been used to treat their infection, however, development of CRO resistance are often associated with plasmid-mediated bla_CMY. Here, we investigated the presence of plasmid-mediated ISEcp-1 tnpA-bla_CMY-2-blc-sugE and the role of these genes in regulation of CRO susceptibility in different hosts.

METHODS

194 strains of Salmonella serovars and Shigella were tested for CRO susceptibility. Non-susceptibility strains were examined for plasmid-mediated ISEcp-1 tnpA-bla_CMY-2-blc-sugE by PCR amplification, Southern blot, and DNA sequencing. The plasmid profiles were determined by HindIII-digested restriction fragment length polymorphism (RFLP). Four recombinant plasmids with different genes from ISEcp-1 tnpA-bla_CMY-2-blc-sugE were constructed and then were transferred into Escherichia coli and different Salmonella serovars to evaluate the CRO susceptibility.

RESULTS

Among 20 CRO-nonsusceptible isolates of Salmonella Choleraesuis (5), S. Typhimurium (4), S. Mons (1), S. Stanley (2) and Shigella sonnei (8) with plasmid-mediated bla_CMY-2, 19 isolates carried the ISEcp-1 tnpA-bla_CMY-2-blc-sugE and only one isolate with tnpA-bla_CMY-2. Transformation of these plasmids into E. coli pir116 produced multidrug resistance. Furthermore, PCR-RFLP analysis determined 5 different plasmid profiles and identical RFLP pattern between S. Typhimurium and S. sonnei. Transformation of the recombinant plasmids into E. coli and different Salmonella serovars resulted in phenotypes ranging from susceptible to resistant (especially inducible resistance) to CRO that were dependent on the genes, and host.

CONCLUSION

The CRO susceptibility associated with the ISEcp-1 tnpA-bla_CMY-2-blc-sugE element is regulated positively by ISEcp-1 tnpA and SugE and negatively regulated by Blc and unknown species-dependent host factor(s).

Research Note: Longitudinal monitoring of chicken houses in a commercial layer farm for antimicrobial resistance in Escherichia coli with special reference to plasmid-mediated quinolone resistance

Plasmid-mediated quinolone resistance (PMQR) genes located on conjugative plasmids can be transferred to other bacteria in the absence of antimicrobial selective pressure. To elucidate the prevalence of resistance, including PMQR in an egg-producing commercial layer farm in western Japan where no antimicrobials were used, minimum inhibitory concentrations (MIC) for a total of 375 Escherichia coli isolates obtained from chicken houses in the farm between 2012 and 2017 were determined using the agar dilution methods. Eighty-seven isolates resistant to oxytetracycline (OTC) accounted for 23.0% of the tested isolates, followed by isolates resistant to dihydrostreptomycin (DSM) (18.4%), sulfisoxazole (18.1%), ampicillin (AMP) (14.4%), trimethoprim (TMP) (14.4%), and nalidixic acid (10.1%). The prevalence rate of multidrug-resistant (MDR) isolates—which are resistant to 3 or more antimicrobial classes, including β-lactams, aminoglycosides, quinolones, folate pathway inhibitors, tetracyclines, and phenicols—was inversely related to the age of chickens at the time of bacterial examination. Probably, the prevalence of MDR isolates in layer chickens may have decreased with age owing to the absence of selective pressure. Furthermore, 45 isolates exhibiting enrofloxacin MICs of more than 0.25 μg/mL were examined for PMQR genes. The transfer of PMQR genes was tested by conjugation analysis. Southern blot analysis of genomic DNA revealed that the qnrS1 (5 isolates), qnrS2 (1 isolate), and qnrS13 genes (1 isolate) were located on plasmids with sizes ranging from approximately 60 to 120 kpb. In 1 of the 5 qnrS1-positive isolates and in an isolate with qnrS13, the qnrS genes were transferred to recipient strains. The plasmid harboring the qnrS1 gene was typed as IncF by PCR-based replicon typing. On this plasmid, the bla_TEM, aadA, tetA, and dfrA1 genes responsible for resistance to AMP, DSM, OTC, and TMP, respectively, were detected. The tetA gene was detected in the plasmid harboring the qnrS13 gene, which was typed as IncI1. These results suggest that despite the low prevalence of quinolone resistance in this farm, various PMQR genes, located on diverse plasmids, exist.

Phylogenetic Diversity, Antimicrobial Susceptibility and Virulence Characteristics of Escherichia coli Isolates from Pigeon Meat

Monitoring resistance to antibiotics in wild animals may assist in evaluating tendencies in the evolution of this major public health problem. The aims of this research work were to determine the patterns of antibiotic resistance in Escherichia coli isolates from the meat of wild or domestically reared pigeons from Spain, to detect the presence of virulence and antibiotic resistance genes, and to carry out a phylogenetic classification of the isolates. Of the 37 E. coli strains tested, 32.43% of them belonged to the B2 phylogenetic group, which is often implicated in extra-intestinal infections. None of the strains showed extended-spectrum beta-lactamase activity. All the isolates presented resistance or reduced susceptibility to two or more antibiotics, with high levels of resistance to β-lactams, aminoglycosides and tetracycline. Ten resistance genes were detected, the most frequent of which were ampC, conferring resistance to ampicillin and aadA, conferring resistance to streptomycin. In total, 97.30% of the strains carried virulence factors (between one and five). The strains from pigeons reared in captivity harboured higher average numbers of resistance and virulence genes than isolates from wild pigeons. Pigeon meat is an important reservoir of E. coli with genes for antibiotic resistance and virulence having the potential to cause disease in humans.

Molecular characteristics of carbapenem-resistant Acinetobacter spp. from clinical infection samples and fecal survey samples in Southern China

Background

Carbapenem resistance among Acinetobacter species has become a life-threatening problem. As a last resort in the treatment of gram-negative bacteria infection, resistance to colistin is also a serious problem. The aim of study was to analyze the mechanism of resistance and perform genotyping of carbapenem-resistant Acinetobacter from clinical infection and fecal survey samples in Southern China.

Methods

One hundred seventy and 74 carbapenem-resistant Acinetobacter were isolated from clinical infection samples and fecal survey samples, respectively. We detected the related genes, including carbapenemase genes (bla_KPC, bla_IMP, bla_SPM, bla_VIM, bla_NDM, bla_OXA-23-like, bla_{OXA-24/40-like}, bla_OXA-51-like, and bla_OXA-58-like), colistin resistance-related genes (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5), a porin gene (carO), efflux pump genes (adeA, adeB, adeC, adeI, adeJ, and adeK), mobile genetic element genes (intI1, intI2, intI3, tnpU, tnp513, IS26, ISAba1, and ISAba125), and the integron variable region. Genotyping was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and dendrogram cluster analysis.

Results

Among the 244 carbapenem-resistant Acinetobacter, the common carbapenemase-positive genes included the following: bla_OXA-51-like, 183 (75.00%); bla_OXA-23-like, 174 (71.30%); bla_NDM-1, 57 (23.40%); and bla_OXA-58-like, 30 (12.30%). The coexistence of mcr-1 and bla_NDM-1 in five strains of A. junii was found for the first time. Eleven distinct carO gene variants were detected in 164 (67.20%) strains, and ten novel variants, which shared 92–99% identity with sequences in the Genbank database, were first reported. Efflux system genes were present in approximately 70% of the isolates; adeABC and adeIJK were observed in 76.23 and 72.13%, respectively. Class 1 integrons were detected in 180 (73.80%) strains and revealed that four gene cassette arrays contained 11 distinct genes. The genotyping by ERIC-PCR demonstrated a high genetic diversity of non-baumannii Acinetobacter, and greater than 90% similarity to A. baumannii.

Conclusions

The bla_NDM-1 gene was identified in up to 77% of the carbapenem-resistant Acinetobacter isolated from fecal survey samples, indicating that the gut might be a reservoir of resistant opportunistic bacteria. Intestinal bacteria can be transmitted through the fecal-hand, which is a clinical threat, thus, the monitoring of carbapenem-resistant bacteria from inpatients’ feces should be improved, especially for patients who have been using antibiotics for a long time.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4423-3) contains supplementary material, which is available to authorized users.

Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors

The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.