Mobile genetic elements profiling, gene flow, and antimicrobial susceptibility profiles, among Pseudomonas aeruginosa isolates, isolated from Al Muthanna hospitals' wound and burn units in Iraq

The prevalence assessment of integrons among multidrug-resistant strains of Pseudomonas aeruginosa receives much-needed attention from this study, as we achieved our desired objective by conducting a thorough analysis on one hundred swabs obtained from burn and clinical cases at the hospitals present in Al Muthanna governorate during November of the year 2021 through to March of the year 2022. By implementing various methodologies encompassing the scrutiny of growth traits and cellular composition as well as executing biochemical assays, a total of 55 isolates were determined to exhibit the existence of P. aeruginosa. When cultured in Hifluoro agar media, Pseudomonas aeruginosa produced diverse hues; particularly noticeable was its blue-green colour. It was discovered through investigation that there were no intI2 and inti3 genes present in those isolated. Findings from this research disclosed that about one-fifth, or precisely twelve out of fifty-five P. aeruginosa strains screened, had an actively expressed Integrase I gene. The association between elevated rates of resistance to multiple antimicrobial agents and the existence of integrons is worth mentioning. Furthermore, the assemblage of isolates that were efficacious in the presence of integrons demonstrated an augmented resistance towards several frequently employed antibiotics like rifampicin and ceftazidime. In conclusion, it can be stated with confidence that a considerable occurrence of integrons can be observed in Pseudomonas aeruginosa strains that display resistance to numerous pharmaceutical agents. Additionally, the discovery of the intI1 gene in a considerable proportion of isolates underscores the effectiveness of integrons in conferring resistance to a variety of antimicrobial agents. These revelations supplement our insight into antibiotic-resistant mechanisms while also underscoring the necessity for viable strategies aimed at halting and preventing bacterial drug resistance.

Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo

Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.

Molecular characteristics of clinical IMP-producing Klebsiella pneumoniae isolates: novel IMP-90 and integron In2147

BACKGROUND

Since the first report of carbapenem-resistant Klebsiella pneumoniae isolates in China in 2007, the prevalence of CRKP and CRE has increased significantly. However, the molecular characteristics of IMP-producing Klebsiella pneumoniae (IMPKp) are rarely reported.

METHODS

A total of 29 IMPKp isolates were collected from a Chinese tertiary hospital from 2011 to 2017. Clinical IMPKp were identified by VITEK^®MS, and further analyzed by whole-genome DNA sequencing with HiSeq and PacBio RSII sequencer. Sequencing data were analyzed using CSI Phylogeny 1.4, Resfinder, PlasmidFinder and the MLST tool provided by the Centre for Genomic Epidemiology. The analysis results were visualized using iTOL editor v1_1. The open reading frames and pseudogenes were predicted using RAST 2.0 combined with BLASTP/BLASTN searches against the RefSeq database. The databases CARD, ResFinder, ISfinder, and INTEGRALL were performed for annotation of the resistance genes, mobile elements, and other features. The types of bla_IMP in clinical isolates were determined by BIGSdb-Pasteur. Integrons were drawn by Snapgene, and the gene organization diagrams were drawn by Inkscape 0.48.1.

RESULTS

Four novel ST type, including ST5422, ST5423, ST5426 and ST5427 were identified. The IMP-4 and IMP-1 were the dominant IMP type. The majority of bla_IMP-carrying plasmids belonged to IncN and IncHI5. Two novel bla_IMP-carrying integrons (In2146 and In2147) were uncovered. A novel variant bla_IMP-90 presented in novel integron In2147 has been identified.

CONCLUSIONS

IMPKp showed low prevalence in China. Novel molecular characteristics of IMPKp have been identified. Continuous monitoring of IMPKp shall also be carried out in the future.

Overexpression of blaGES-1 due to a strong promoter in the class 1 integron contributes to decreased ceftazidime-avibactam susceptibility in carbapenem-resistant Pseudomonas aeruginosa ST235

Sequence type 235 (ST235) Pseudomonas aeruginosa, harboring so-called international, high-risk, or widespread clones, is associated with relatively high morbidity and mortality, partly due to multiantibiotic and high-level antibiotic resistance. Treatment of infections caused by such strains with ceftazidime-avibactam (CZA) is often successful. However, CZA resistance in carbapenem-resistant P. aeruginosa (CRPA) strains has been consistently reported with the increasing use of this drug. Likewise, we identified thirty-seven CZA-resistant ST235 P. aeruginosa strains from among 872 CRPA isolates. A total of 10.8% of the ST235 CRPA strains were resistant to CZA. Site-directed mutagenesis, cloning, expression, and whole-genome sequencing analysis revealed that overexpression of bla_GES-1, which was carried in a class 1 integron of the complex transposon Tn6584, occurred due to a strong promoter, contributing to CZA resistance. Moreover, such overexpression of bla_GES-1 combined with an efflux pump resulted in high-level resistance to CZA, considerably reducing the therapeutic options available for treating infections caused by ST235 CRPA. Considering the widespread presence of ST235 P. aeruginosa strains, clinicians should be aware of the risk of CZA resistance development in high-risk ST235 P. aeruginosa. Surveillance initiatives for preventing further dissemination of high-risk ST235 CRPA isolates with CZA resistance are essential.

High frequency of NDM-1 and OXA-48 carbapenemase genes among Klebsiella pneumoniae isolates in central Iran

BACKGROUND

The emergence and distribution of multidrug-resistant (MDR) and carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a global health threat. Therefore, this study aimed to investigate the frequency and antibiotic resistance patterns of MDR, extensively drug-resistant (XDR), and CRKP, as well as the antibiotic resistance genes of Klebsiella pneumoniae (K. pneumoniae) isolates from patients' infectious samples from central Iran.

METHODS

This study examined 546 clinical samples of patients to identify K. pneumoniae. The isolates were investigated for their antibiotic resistance profile, extended-spectrum β-lactamase (ESBL), AMPC β-lactamase, carbapenemase resistance, sulfonamide, tetracycline, plasmid-mediated quinolone resistance (PMQR) along with their resistance genes, integrase, and quaternary ammonium compounds (qac) by polymerase chain reaction (PCR).

RESULTS

Out of 546 clinical samples, 121 (22.1%) cases of K. pneumoniae were identified using culture and PCR methods. The highest antibiotic resistance rates were found for ampicillin (119/121; 98.3%), cotrimoxazole (78/121; 64.4%), and cefixime, cefotaxime, ceftriaxone, and ceftazidime as a group (77/121; 63.6%). Tigecycline, colistin, and fosfomycin were the most effective antimicrobial agents with 98.4%, 96.7%, and 95.9% susceptibility, respectively. The amount of CRKP was 51 (42.1%). All CRKP isolates were MDR. The most abundant genes were bla_TEM (77/77; 100%), bla_CTX-M1 (76/77; 98.7%), bla_SHV (76/77; 98.7%), bla_CTX-M15 (73/77; 94.8%) for ESBL; bla_CIT 28 (48.3%) and bla_CMY-2 26 (44.8%) for AMPC β-lactamase; and bla_OXA-48 46 (90.1%) and bla_NDM 36 (70.5%) for carbapenemase. Among the PMQR determinants, qnrB (25/52; 48%), qnrS (19/52; 36.5%), and qnrA (11/52; 21.1%) were positive from the isolates. TetA and tetB were recognized in 25 (44.6%) and 17 (30.3%) isolates, respectively. Class 1 and 2 integrons were recognized in 97 (80.1%) and 53 (43.8%) isolates, respectively.

CONCLUSIONS

Due to the high prevalence of MDR and CRKP in central Iran, tracking and immediate intervention are necessary for control and inhibition of K. pneumoniae resistant isolates. Tigecycline, colistin, and fosfomycin are the best treatment options for treatment of patients with CRKP in this geographical area.

Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects

Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.

Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors

The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.

Molecular characterization of class 1 integrons in carbapenem-resistant Enterobacterales isolates

OBJECTIVE

Carbapenem-resistant Enterobacterales (CRE) infections result in higher treatment costs and mortality rates. Integrons play important roles in emergence and spread of antibiotic resistant genes. To get a better understand on the effects of integron on CRE resistance, distribution of common carbapenemase genes and class 1 integron in clinical CRE isolates were investigated.

METHOD

Carbapenemase genes, including bla_KPC, bla_VIM, bla_IMP, bla_NDM, bla_GES, bla_VEB and bla_OXA-23, were screened in 161 CRE isolates and subtypes of these genes were confirmed through sequence analysis. Class 1 integron was screened and common promoter and gene cassette arrays were determined by sequencing. The resistant rates to clinical commonly used antibiotics between integron positive and integron negative CRE isolates were compared.

RESULTS

Of 161 CRE isolates, the most prevalent carbapenemase gene was bla_KPC-2, which was detected in 139 isolates, including 99 Klebsiella pneumoniae. Class 1 integron was detected in 78 isolates. Twenty different gene cassettes, including two carbapenemase genes bla_VEB-1 and bla_IMP-4, and nine different gene cassette arrays, including bla_VEB-1-aadB-arr-2-cmlA5-bla_OXA-10-aadA1, aadB-catB8-bla_OXA-10-aadA1-dfrA1-aacA4 and bla_IMP-4-qacG-aacA4-catB3, were detected. Five types of common promoters were identified. Relative weak promoter PcH1 was the dominant type. Resistant rates of CRE isolates containing class 1 integrons to ceftazidime, amikacin, trimethoprim/sulfamethoxazole and gentamicin were higher than those without class 1 integrons (P < 0.05).

CONCLUSION

Class 1 integrons play important roles in the emergence and spread of CRE resistance. To the best of our knowledge, this is the first report of aadB-catB8-bla_OXA-10-aadA1-dfrA1-aacA4 and bla_IMP-4-qacG-aacA4-catB3 in the same Providencia rettgeri isolate and bla_VEB-1-aadB-arr-2-cmlA5-bla_OXA-10-aadA1 in P. rettgeri.

Detection of multidrug resistant pathogenic bacteria and novel complex class 1 integrons in campus atmospheric particulate matters

Recent advances provided overwhelming evidence that atmospheric particulate matters carry a substantial amount of antibiotic resistance genes (ARGs). It has also been documented that polluted air facilitates transmission of bacterial pathogenesis and antimicrobial resistance (AMR). These investigations generally used culture-independent approaches which reveal sophisticated microbiomic and resistomic compositions in particulate matters, while culture-dependent methods directly demonstrating presence of live, functional bacteria has not been fully applied. In recent years, efforts undertaken worldwide managed to reduce air particulate matter pollution, leading to cleaner air in many parts of world, including China. Whether atmospheric particulate matters may still function as vehicles for pathogenic bacteria and AMR in improving air conditions is turning into an interesting question to address. In attempt to answer this question, a culture-dependent approach is used to find out the putative role of atmospheric particulate matters in relatively 'clean' air to transmit pathogenic bacteria and AMR in this work. By harvesting particulate matters in an unindustrialized and less-polluted university campus, culturing and identifying bacteria in particulate matters, and characterizing pathogenesis and AMR properties of these bacteria, interesting findings were made that even in relatively 'clean' air, antibiotic-resistant pathogenic bacteria are prevalent; and that mobile genetic elements including integrons are widespread. In particular, in air samples collected, multidrug-resistant hemolytic Bacillus strains that may pose significant health threat could be identified. Complex class 1 integrons, two of which carry novel antibiotic resistant gene cassette arrays, were also found for the first time in airborne bacteria, suggesting the danger of horizontal transfer of AMR in air. In conclusion, using culture-dependent methods, this work shows that atmospheric particulate matters are viable vehicles for the transmission of bacterial pathogenesis and AMR, and that even in relatively 'clean' air, the threat of airborne antibiotic-resistant pathogens is significant.

Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae

Vibrio cholerae N16961 genome encodes 18 type II Toxin/Antitoxin (TA) systems, all but one located inside gene cassettes of its chromosomal superintegron (SI). This study aims to investigate additional TA systems in this genome. We screened for all two-genes operons of uncharacterized function by analyzing previous RNAseq data. Assays on nine candidates, revealed one additional functional type II TA encoded by the VCA0497-0498 operon, carried inside a SI cassette. We showed that VCA0498 antitoxin alone and in complex with VCA0497 represses its own operon promoter. VCA0497-0498 is the second element of the recently identified dhiT/dhiA superfamily uncharacterized type II TA system. RNAseq analysis revealed that another SI cassette encodes a novel type I TA system: VCA0495 gene and its two associated antisense non-coding RNAs, ncRNA495 and ncRNA496. Silencing of both antisense ncRNAs lead to cell death, demonstrating the type I TA function. Both VCA0497 and VCA0495 toxins do not show any homology to functionally characterized toxins, however our preliminary data suggest that their activity may end up in mRNA degradation, directly or indirectly. Our findings increase the TA systems number carried in this SI to 19, preferentially located in its distal end, confirming their importance in this large cassette array.

A comparative study on antibiotic resistance and virulence properties of Staphylococcus aureus isolated from hospitalized patients and hospital environment

BACKGROUND

We compared the characteristics of clinical Staphylococcus aureus and S. aureus isolated from environmental surfaces in 3 hospitals.

METHODS

Clinical S. aureus isolates were collected from hospitalized patients. Environmental surfaces were sampled from the rooms of patients infected with S. aureus. After identifying rooms with the target organism, 3-5 high-touch surfaces in patient care areas were sampled using swabs before room cleaning by environmental services. S. aureus isolates were subjected to genotyping, antimicrobial susceptibility testing, and virulence determinant screening. The isolates were analyzed for integron content and sequences of variable region amplification products.

RESULTS

There were epidemiologically unrelated 79 clinical and 62 environmental S. aureus isolates. Overall, 11.4% of clinical and 59.7% of environmental isolates were methicillin-resistant. The environmental and clinical S. aureus exhibited very different virulence profiles: 79% of the environmental isolates were negative for virulence genes compared to 2.5% of clinical isolates (P < .001). Environmental isolates were more resistant to antibiotics compared to clinical isolates. Class 1 integrons were only detected in 7 of 62 environmental isolates, of which 3 isolates had integrons with cysteine synthase cassette, 1 had aadA1, and 1 had an unknown cassette.

CONCLUSION

These data indicate the different characteristics between environmental and clinical S. aureus, which may reflect different reservoirs from which the 2 groups acquired the strains.

Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils

Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10^-7 to 1.0 × 10^-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10^-6 to 2.85 × 10^-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.

Unravelling complex transposable elements surrounding bla(GES-16) in a Pseudomonas aeruginosa ExoU strain

OBJECTIVES

We characterised the complex surrounding regions of bla_GES-16 in a Pseudomonas aeruginosa exoU+ strain (P-10.226) in Brazil.

METHODS

Species identification was performed by MALDI-TOF MS, and the antimicrobial susceptibility profile was determined by broth microdilution based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The whole genome sequencing (WGS) of P-10.226 strain was performed using both short-read paired-end sequencing on the Illumina MiSeq platform as well as the long-read Oxford Nanopore MinION.

RESULTS

WGS analysis showed that P-10.226 carried bla_GES-16, which was found as a gene cassette inserted into a novel class I integron, In1992 (aadB-bla_OXA-56-bla_GES-16-aadB-aadA6c), whose 3'-CS was truncated by a nested transposable element, IS5564::ISPa157. The structure was even more complex since IS6100-ΔIS6100 structure and a TnAs2-like harbouring the operon merRTPADE was found downstream In1992. Fragments of TnAs3 harbouring 25-bp imperfect inverted repeats were identified bordering the intl1 of In1992 and also flanking IS6100-ΔIS6100, which might be genetic marks of its previous presence in the genome. Interestingly, In1992 also shows a distinct cassette array from In581 (bla_GES-16-dfrA22-aacA27-aadA1), which was previously reported in Serratia marcescens strains recovered in Brazil. Finally, exoU gene, which encodes a potent cytotoxin of type III secretion systems (T3SS) effector proteins from P. aeruginosa and is associated to severe infections, was also detected.

CONCLUSION

We described the novel In1992 carrying bla_GES-16 surrounded by complex transposition events in a XDR P. aeruginosa strain. The identification of many sets of direct repeats adjacent to TnAs3 fragments indicates a major past of transposition events that shaped the current genetic environment of In1992.

Prevalence, Antimicrobial Susceptibility and Resistance Gene Detection in Bacteria Isolated from Goldfish and Tiger Barb from Ornamental Fish Farms of Tamil Nadu

This study aims to determine the antimicrobial resistance (AMR) pattern in freshwater ornamental cyprinids, such as Goldfish and Tiger barb. Molecular characterization of bacterial isolates confirmed the presence of 7 bacterial isolates in Goldfish and 6 in Tiger barb. Antimicrobial susceptibility test using 36 antibiotics revealed a higher resistance pattern for bacitracin, rifampicin, trimethoprim, cefalexin, ampicillin, amoxicillin, nalidixic acid and nitrofurantoin. Sulphafurazole, norfloxacin and ciprofloxacin were effective against all the bacterial isolates derived from Goldfish and Tiger barb. Most bacterial isolates exhibited > 0.2 multi-drug resistance index (MDR), indicating the severity of antibiotic use in the culture system. The finding of the present study suggests that ornamental fish may act as the reservoir of MDR bacteria and dissemination of resistance genes to clinical and human commensal bacteria through horizontal gene transfer.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01023-y.

Multi-drug resistance, integron and transposon-mediated gene transfer in heterotrophic bacteria from Penaeus vannamei and its culture environment

Multi-drug resistance (MDR) in bacteria is regarded as an emerging pollutant in different food production avenues including aquaculture. One hundred and sixty out of 2304 bacterial isolates from shrimp farm samples (n = 192) of Andhra Pradesh, India, were MDR. Based on biochemical identification and 16S rRNA sequencing, they were grouped into 35 bacterial species with the predominance of Vibrio parahaemolyticus (12.5%). The MDR isolates showed highest resistance toward oxytetracycline (89%) with more than 0.2 MAR (multiple antibiotic resistance), demonstrates a high-risk source. The most prevalent antibiotic-resistance gene (ARG) and mobile genetic element (MGE) detected were tetA (47.5%) and int1 (46.2%), respectively. In conjugation experiments, overall transfer frequency was found to be in the range of 1.1 × 10^-9 to 1.8 × 10^-3 with the transconjugants harbouring ARGs and MGEs. This study exposed the wide distribution of MDR bacteria in shrimp and its environment, which can further aggravate the already raised concerns of antibiotic residues in the absence of proper mitigation measures.

Distribution of Class 1-3 Integrons in Carbapenem-Resistant Pseudomonas aeruginosa Isolated from Inpatients in Shiraz, South of Iran

Background

Health-care-associated infection (HAI) is effect on patients for the time of staying in the hospital. Opportunistic pathogens including Pseudomonas aeruginosa are the most dangerous biological agents in nosocomial infections. This study aimed to assess the prevalence of 3 classes of integrons carrying to carbapenem resistance in P. aeruginosa strains collected from Nemazee hospital.

Methods

This cross-sectional study was conducted on clinical P. aeruginosa isolates were collected from Nemazee hospital. The identification of the isolates was performed by routine biochemical tests. Antimicrobial sensitivity testing was determined using the disk diffusion method against imipenem and meropenem. The int1, int2 and int3 genes were detected using the polymerase chain reaction (PCR).

Results

Seventy-five clinical isolates of P. aeruginosa were recovered from various clinical infections. A carbapenem-resistant phenotype was detected in 42.7% (imipenem) and 29.3% (meropenem) of isolates. As the PCR results, 48 (64%) and 15 (20%) isolates were identified as being positive for class 1 and class 2 integrons, respectively. Class 3 integrons were not found among the studied isolates.

Conclusions

Our data demonstrate the importance of class 1 and 2 integrons in carbapenem resistant P. aeruginosa strains. Therefore, integrons play an important role in acquisition and dissemination of carbapenem resistance genes among these pathogens, so, management of infection control policies and the appropriate use of antibiotics is essential for control the spreading of antibiotics resistance genes.

High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several β-lactamase and integron genes collected from several hospitals in the north of Iran

Background

Klebsiella pneumoniae is one of the leading causes of hospital outbreaks worldwide. Also, antibiotic-resistant K. pneumoniae is progressively being involved in invasive infections with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the incidence of resistance genes (integron types and β-lactamase-encoded genes) among clinical isolates of K. pneumoniae.

Methods

In this cross-sectional study, a total of 100 clinical samples were obtained from hospitalized patients in three teaching hospitals in the north of Iran, from November 2018 and October 2019. Antimicrobial susceptibility testing was performed using disk agar diffusion test in line with CLSI recommendations. For colistin, minimum inhibitory concentration (MIC) was determined using broth microdilution. Based on antibiogram, multi-drug resistant (MDR) and extensive-drug resistant (XDR) strains were detected. Finally, integron types and β-lactamase resistance genes were identified using polymerase chain reaction technique.

Results

The most and least clinical samples were related to the urine and bronchoalveolar lavage, respectively. Based on the antibiogram results, amikacin and gentamicin exhibited good activity against K. pneumoniae strains in vitro. The high resistance rate (93%) to ampicillin/sulbactam predicts the limited efficacy of this antibiotic, in the hospitals studied. Among all the 100 isolates, the frequency of MDR and XDR phenotypes were 58% and 13%, respectively, while no pan-drug resistant (PDR) strains were found. In the MDR K. pneumoniae strains, the prevalence of bla_SHV, bla_TEM, bla_CTX-M-15, bla_KPC, bla_OXA-48, bla_NDM β-lactamase genes were 91.4%, 82.7%, 79.3%, 29.3%, 36.2% and 6.9%, respectively, however 91.4% of the isolates were carrying intI gene. Class II and III integrons were not detected in any isolates.

Conclusion

The MDR K. pneumoniae is becoming a serious problem in hospitals, with many strains developing resistance to most available antimicrobials. Our results indicate co-presence of a series of β-lactamase and integron types on the MDR strains recovered from hospitalized patients. The increasing rate of these isolates emphasizes the importance of choosing an appropriate antimicrobial regimen based on antibiotic susceptibility pattern.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00476-1.

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

First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis

OBJECTIVES

Klebsiella michiganensis is an emerging pathogen. Like Klebsiella pneumoniae, this species is able to acquire antibiotic resistance genes (ARGs) via mobile genetic elements. In this context, K. michiganensis isolates producing carbapenemases of KPC, NDM, IMP and OXA-48-like types have already been reported. Here we characterised a strain (BD-50-Km) isolated from a rectal swab of a Turkish patient hospitalised in Switzerland.

METHODS

Species identification was initially performed using MALDI-TOF/MS. Antimicrobial susceptibility testing was done by the microdilution method. Whole-genome sequencing (WGS) was performed with both Illumina and Nanopore platforms and was used to confirm species identification, to characterise plasmids and to perform core-genome analyses.

RESULTS

BD-50-Km was initially identified as Klebsiella oxytoca and showed reduced susceptibility to imipenem. However, WGS indicated that the isolate was actually K. michiganensis. BD-50-Km carried the bla_VIM-1 gene associated with a rare class 1 integron (In87) located on a pST1 196 kb IncC plasmid. This plasmid shares its backbone with many other IncC plasmids found in different species (including five K. michiganensis), but not the same In87 and the remaining region harbouring various ARGs. BD-50-Km belongs to the novel ST342. Moreover, core-genome analysis (single nucleotide variant analysis) showed that BD-50-Km was not closely related to any K. michiganensis strains deposited in NCBI (n = 212), including the 38 so far reported as possessing carbapenemase genes.

CONCLUSION

This is the first report of a bla_VIM-possessing K. michiganensis clinical isolate. The spread of plasmid-mediated VIM carbapenemases in this emerging pathogen represents an additional threat to our therapeutic armamentarium.

Integron Identification in Bacterial Genomes and Cassette Recombination Assays

Integrons are genetic elements involved in bacterial adaptation to the environment. Sedentary chromosomal integrons (SCIs) can stockpile and rearrange a myriad of different functions encoded in gene cassettes. Through their association with transposable elements and conjugative plasmids, some SCIs have acquired mobility and are now termed Mobile Integrons (MIs). MIs have reached the hospitals and are involved in the rise and spread of antibiotic resistance genes through horizontal gene transfer among numerous bacterial species. Here we aimed at describing methods for the detection of integrons in sequenced bacterial genomes as well as for the experimental characterization of the activity of their different components: the integrase and the recombination sites.

Zhang et al

An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.

New insights regarding Acinetobacter genomic island-related elements

The objective of this study was to mobilise the Acinetobacter genomic island 1-A (AGI1-A) from Enterobacter hormaechei EclCSP2185 (E. cloacae complex) and to search for the distribution and structure of AGI1-related elements in the NCBI database. AGI1-A was transferred to Escherichia coli. Analysis of the attachment (att) sites could locate the possible recombination crossover in the att sequences at position 10-11 (GG) in the last 18 bp of trmE. In silico detection of AGI backbones in the WGS database identified AGI variants in Salmonella enterica (83 strains), Vibrio cholerae (33), E. hormaechei (12), Acinetobacter baumannii (2), most belonging to prevalent clones (ST40, ST69, ST114 and ST25, respectively), but also in E. coli (1) and Klebsiella pneumoniae (1). Two groups of backbone were identified: one similar to AGI1, the other with a short segment from a Shewanella element upstream of ORF A022. The MDR regions were inserted by transposition at the res site in four different positions ATAGG (A. baumannii), CATAG (S. enterica and V. cholerae), TAGGT (S. enterica and K. pneumoniae) and TGCAC (S. enterica) representing four different lineages. In some V. cholerae, E. hormaechei and E. coli, deletion events occurred that eliminated part of the backbone at the left junction. Analysis of the right junction identified a fifth lineage in V. cholerae and E. hormaechei (CCATA). In conclusion, based on the position of the MDR region, AGI-related elements belonged to five groups of closely related genomic islands (AGI1-AGI5), with differences in backbones that evolved independently over time.

Prevalence of class 1 integron in Escherichia coli isolated from animal sources in Iran: a systematic review and meta-analysis

Background

Among the genetic elements, integrons may contribute to the widespread incidence and spreading of antibiotic resistance among Escherichia coli isolates. Accordingly, this review aims to investigate the prevalence of class 1 integron in E. coli isolated from animal sources in Iran.

Methods

This systematic literature search was performed from January 1, 2000 to the end of May 1, 2019.

Then, publications that met our inclusion criteria were selected for data extraction and analysis. Also, the quality of included studies was independently assessed by two researchers based on the Joanna Briggs Institute. Meta-analysis was performed by the Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran’s Q, and I² tests. Publication bias was estimated by funnel plot and Egger’s linear regression test.

Results

Based on inclusion criteria, five studies were included to meta-analysis. From those studies, the pooled prevalence of integrons was 33% (95% CI, 23.8–43.7%) ranging from 23.8 to 52.4%. There was a significant heterogeneity among the 5 studies (χ² = 11.73; p < 0.019; I² = 65.91%). Additionally, Begg’s and Egger’s tests were performed to quantitatively evaluate the publication biases. According to the results of Begg’s test (z = 1.22, p = 0.22) and Egger’s test (t = 3.03, p = 0.056), a significant publication bias was not observed.

Conclusions

Our finding revealed the relatively high prevalence of class 1 integrons among E. coli isolates. Moreover, there was a significant heterogeneity among studies and subgroup analysis also showed that there was no difference about prevalence of class 1 integrons among different sample source.

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities

BACKGROUND

New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics.

RESULTS

We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now.

CONCLUSION

To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.

Correlation of quinolone-resistance, qnr genes and integron carriage in multidrug-resistant community isolates of Klebsiella spp

Objectives

Plasmid-mediated quinolone resistance (PMQR) determinants and integrons have a considerable contribution to bacterial drug resistance in Gram-negative pathogens. We studied the prevalence of PMQR genes and integron carriage in multidrug-resistant community isolates of Klebsiella spp.

Materials and Methods

Two hundred and fifty Klebsiella spp. isolates were collected from outpatient specimens between August 2015 and October 2017 in Yazd central Laboratory, Iran. Antibiotic susceptibility was determined against 17 antibiotics and minimum inhibitory concentration (MIC) of ciprofloxacin was measured by E-test. Polymerase chain reaction (PCR) was employed for detection of qnrA, qnrB, qnrS, aac(6')-Ib-cr, oqxAB and qepA genes.

Results

Disc diffusion results showed that 17 isolates (6.8%) were multidrug resistant (MDR), two of which were Klebsiella oxytoca and 15 were Klebsiella pneumoniae. MIC measurements revealed 11 ciprofloxacin-resistant isolates (including the two K. oxytoca), three intermediately-resistant and three ciprofloxacin-susceptible isolates. All ciprofloxacin-resistant and intermediately-resistant isolates carried at least one and up to four PMQR genes. The most prevalent PMQR gene was oqxAB (93.75%) followed by aac(6')-ib-cr (50.0%), qnrB (25.0%) and qnrS (18.75%) but qnrA and qepA were not detected. Class 1 integron was observed in 14 (82.3%) isolates including nine ciprofloxacin-resistant, two intermediately-resistant, and three susceptible isolates. Class 2 and 3 integrons were not observed.

Conclusion

Presence of MDR, multiple PMQR determinants as well as class 1 integron in community isolates of Klebsiella spp. can be an important source of transmission of these opportunistic pathogens.

coli</i>, Sana'a Hospitals, Yemen

BACKGROUND AND OBJECTIVES

The occurrence of multi-drug resistance (MDR) Escherichia coli is one responsible for raised mortality and morbidity and was reported as major health problem. Class 1 integrons has crucial role in distributing antibiotic resistance genes among bacteria. Present work was aimed to determine the prevalence of class 1 integrons and its association with antibiotic resistance in MDR E. coli isolated from patient's body fluid and tissues from 6 health centers in Sana'a, Yemen.

MATERIALS AND METHODS

A cross-sectional study a total of 198 E. coli from patients diagnosed with infection that had been referred to 6 hospitals and medical diagnostic from July, 2017 to August, 2017 in Sana'a, Yemen. Susceptibility of E. coli isolates to 15 antibiotics using the disc diffusion method. Conventional polymerase chain reaction was used for detection of class 1 of integrons in 100 randomly selected MDR E. coli.

RESULTS

Overall 174 (87.9%) of 198 E. coli isolates were MDR. Class 1 integrons were detected in 67% of the randomly selected 100 of 198 MDR E. coli. A significant range (p<0.05-p<0.0001) was identified between presence of class 1 integrons and resistance to ceftriaxone, aztreonam, cefepime, amoxicillin-clavulanic acid, cefotoxime, cefepime-clavulanic acid, ceftazidime-clavulanic acid, ciprofloxacin, ceftazidime, norfloxacin and trimethoprim-sulfamethoxazole, while no significant difference were identified between integron class 1 and resistance to gentamicin, amikacin, nitrofurantoin and imipenem.

CONCLUSION

High MDR E. coli isolates were detected in this study, among them the prevalence of class 1 integrons is the most common. The significant association between class 1 integrons and resistance to common prescribed antibiotics in hospitals in Sana'a, Yemen.

Genotypes, carbapenemase carriage, integron diversity and oprD alterations among carbapenem-resistant Pseudomonas aeruginosa from Russia

Pseudomonas aeruginosa is a serious opportunistic pathogen demonstrating a high level of resistance to many groups of antibiotics, including carbapenems. This study aimed to characterise the molecular epidemiology and prevalence of mobile genetic elements associated with resistance to carbapenems among P. aeruginosa (CRPA) clinical isolates. Among 145 carbapenem-resistant P. aeruginosa isolates, 34 different sequence types (STs) were detected; the six most common STs were ST654 (24%), ST235 (24%), ST111 (8%), ST446 (6%), ST357 (5%) and ST2592 (a novel single-locus variant of ST357) (4%). A carbapenemase gene was found in 94 isolates (64.8%). The bla_VIM-2 gene was harboured by 64 isolates (44.1%) restricted to ST111, ST235 and ST654, and the bla_GES-type and bla_OXA-10 group genes were each detected in 15 isolates (10.3%); none of other tested carbapenemase genes, including bla_IMP, bla_NDM and bla_GIM, were detected. Among the bla_VIM-2-positive isolates, five types of bla_VIM-2-containing integrons were discovered, including In56, In559, In59-like, In59 and In249. The oprD gene was disrupted by an insertion sequence (IS) in 15.9% of isolates. Overall, five types of IS elements were found (ISPsme1, ISPa1328, ISPa26, ISPst2 and ISPa195). Observed rearrangements within variable regions of bla_VIM-2-carrying integrons in conjunction with the discovery of a novel type of oprD-disrupting IS element illustrate the ongoing evolution of CRPA a, which warrants further investigation.

Dynamics of metal(loid) resistance genes driven by succession of bacterial community during manure composting

Metal(loid) resistance genes (MRGs) play important roles in conferring resistance to metal(loid)s in bacterial communities. How MRGs respond to bacterial succession during manure composting remains largely unknown. Metagenomics was used in the present study to investigate the compositional changes of MRGs, their candidate hosts and association with integrons during thermophilic composting of chicken manures. MRGs conferring resistance to 20 metal(loid)s were detected, and their diversity and abundance (normalized to the abundance of 16S rRNA genes) were significantly reduced during composting. MRGs associated with integron were exclusively observed in proteobacterial species. Class 1 integron likely played an important role in maintaining mercury-resistance mer operon genes in composts. Escherichia coli harbored the most abundant MRGs in the original composting material, whereas species of Actinobacteria and Bacilli became more important in carrying MRGs during the late phases. There were significant linear relationships between the relative abundance of some specific bacterial species (E. coli, Actinobacteria species and Enterococcus faecium) and the abundance of MRGs they potentially harbored. The succession of these bacteria contributed to an overall linear regression between the relative abundance of all predicted candidate hosts and the abundance of total MRGs. Our results suggest that the succession of bacterial community was the main driver of MRG dynamics during thermophilic composting.

Study of genetic diversity, biofilm formation, and detection of Carbapenemase, MBL, ESBL, and tetracycline resistance genes in multidrug-resistant Acinetobacter baumannii isolated from burn wound infections in Iran

Background

Antimicrobial resistance in multidrug-resistant Acinetobacter baumannii (MDR-AB) isolated from burn wound infections is a major concern in intensive care or burns units worldwide, and molecular studies are considered critical strategies for control of MDR-AB outbreaks in this regard. Thus, in this study, antibiotic resistance, biofilm-forming ability, molecular epidemiology of MDR A. baumannii strains recovered from patients with burns were investigated in three major hospital centers of Iran.

Methods

In this cross-sectional research, 163 non-repetitive A. baumannii strains were tested for susceptibility to antimicrobial agents. Polymerase chain reaction (PCR) was performed to characterize ambler classes A, B, and D β-lactamases, ISAba1 and integrons, biofilm formation was also investigated. Clonal relatedness was analyzed using Pulsed-Field Gel Electrophoresis (PFGE).

Results

Among 163 A. baumannii strains collected, 94.5% of them were Carbapenem-Non-Susceptible A. baumannii (CNSAB) and also 90.1 and 52.2% of them were Metallo-β-Lactamases (MBL) and Extended-Spectrum β-Lactamases (ESBL) producing isolates, respectively. Colistin and polymyxin B exhibited excellent activity against CNSAB strains. High prevalence of bla_{OXA − 23-like} (85.1%), bla_VIM (60.5%), bla_{PER − 1} (42.3%), tetB (67.8%), and Class 1 integrons (65.6%) were identified in CNSAB strains. ISAba1 element was associated with 42 (25.8%) and 129 (98.5%) of bla_OXA-51-like and bla_OXA-23-like genes, respectively. 6 clusters with the ability to form strong biofilms were found to be dominant and endemic in our entire areas.

Conclusions

Results of the present study show that antimicrobial resistance in CNSAB isolates from burn wound infections in monitored hospitals in Iran is multifactorial, and also findings of the study suggested that local antibiotic prescription policies should be regularly reviewed, and efficient infection control measures should be observed. Therefore, further strengthening of surveillance of antimicrobial resistance is urgently needed in these regions.

Virulence characteristics of multidrug resistant biofilm forming Acinetobacter baumannii isolated from intensive care unit patients

Background

Nosocomial infections and persistence of multidrug resistant biofilm forming Acinetobacter baumannii in hospitals has made it as a serious problem in healthcare settings worldwide.

Methods

A total of 100 A. baumannii clinical isolates from immunocompromised patients hospitalized in ICU were investigated for biofilm formation, the presence of biofilm related genes (bap, ompA, csuE, fimH, epsA, bla_PER-1, bfmS, ptk, pgaB, csgA, kpsMII), integron characterization and molecular typing based on REP-PCR.

Results

All isolates were resistant to three or more categories of antibiotics and considered as multidrug resistant (MDR). A total of 32 isolates were resistant to all tested antibiotics and 91% were extensively drug-resistance (XDR). All isolates were able to produce biofilm and 58% of isolates showed strong ability to biofilm formation. All strong biofilm forming A. baumannii isolates were XDR. All A. baumannii isolates carried at least one biofilm related gene. The most prevalent gene was csuE (100%), followed by pgaB (98%), epsA and ptk (95%), bfmS (92%) and ompA (81%). 98% of isolates carried more than 4 biofilm related genes, simultaneously. Class I integron (67%) was more frequent in comparison with class II (10%) (P < 0.05). The REP-PCR patterns were classified as 8 types (A-H) and 21 subtypes. The A1 (23%) and C1 (15%) clusters were the most prevalent among A. baumannii isolates (P < 0.05). According to the REP-PCR patterns, 23% of all isolates had a clonal relatedness.

Conclusion

Our study revealed the high frequency of biofilm forming XDR A. baumannii in ICU patients, with a high prevalence of biofilm related genes of csuE and pgaB. It seems that the appropriate surveillance and control measures are essential to prevent the emergence and transmission of XDR A. baumannii in our country.

Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus)

Increasing reports of antimicrobial resistance in wildlife highlight the significance of a One Health approach to managing resistance. We investigated the prevalence and diversity of class 1 integrons, a genetic determinant of resistance, in grey-headed flying foxes, a large fruit bat species belonging to the order Chiroptera. Class 1 integrons were detected in both wild flying foxes (5.3%) and captive flying foxes (41.2%) housed in wildlife rehabilitation facilities. Genes encoding resistance to aminoglycosides, trimethoprim and beta-lactams, and Qac efflux pumps were detected. Analysis of conserved integron elements and gene cassette arrays indicate the direction of integron transfer is from humans to flying foxes. The detection of two novel gene cassette arrays (5'CS-qacH-aacA34-bla_OXA-21-3'CS and 5'CS-qacF-3'CS strongly suggests acquisition of genes from the environmental resistome into class 1 integrons within the flying fox microbiota. The dynamics of class 1 integrons in flying foxes indicates bats have a role in the emergence of novel antibiotic resistance determinants.

The new perspective of old antibiotic: In vitro antibacterial activity of TMP-SMZ against Klebsiella pneumoniae

BACKGROUND/PURPOSE

Trimethoprim-sulfamethoxazole (TMP-SMZ) is broadly administered to treat multiple infections, and the paucity of effective treatment alternatives for infections caused by Klebsiella pneumoniae has led to a renewed interest in TMP-SMZ. The aim of this study is to evaluate the antibacterial efficacy of TMP-SMZ against K. pneumoniae.

METHODS

The resistance genes of K. pneumoniae clinical isolates were investigated by PCR, followed by conjugation experiments and multilocus sequence typing.

RESULTS

The resistance rate of K. pneumoniae to TMP-SMZ decreased over the collection period from 26.7% (88/330) to 16.9% (56/332). The high carrying rates (173/175, 98.9%) of resistance determinants (sul genes or dfr genes) were the main mechanisms of TMP-SMZ resistance isolates, with sul1 (142/175, 81.1%) and dfrA1 (119/175, 68.0%). Only class 1 integron was detected, the prevalence of which in TMP-SMZ resistant K. pneumoniae was 63.4% (111/175).

CONCLUSION

These results provided insights into the antimicrobial efficacy of TMP-SMZ against K. pneumoniae, also illustrating the wide distribution of SMZ and TMP resistance genes among resistant K. pneumoniae. Simultaneously, the present study highlights the significance of reasonable administration and effective continued monitoring.

Plasmid-located dfrA14 gene in Pasteurella multocida isolates from three different pig-producing farms in Germany

Pasteurella multocida is an important respiratory tract pathogen in intensive livestock farming, especially in pigs. Antimicrobial agents are frequently used to combat infections caused by this pathogen. In a study on antimicrobial resistance among respiratory tract pathogens of pigs from 30 German pig-producing farms, P. multocida isolates (n = 9) with high minimal inhibitory concentration (MIC) values of 16/304 mg/L (n = 2), 32/608 mg/L (n = 3) or ≥64/1216 mg/L (n = 4) for trimethoprim/sulfamethoxazole (1:19) and of ≥512 mg/L (n = 9) for trimethoprim (TMP) were detected in three of these farms. The genetic relatedness of the isolates was investigated via capsule-specific PCR and macrorestriction analyses with ApaI and SmaI. Pulsed-field gel electrophoresis revealed indistinguishable restriction patterns per farm, with slight differences between the three farms. All isolates represented capsular type A. Four representative isolates, that were subjected to whole genome sequencing, shared the multi-locus sequence type (ST) 3. Their plasmids were transformed into E. coli TOP10 with subsequent selection on TMP-containing agar plates. Antimicrobial susceptibility testing and plasmid analysis of the transformants confirmed that they were resistant to sulfonamides and trimethoprim and carried only a single small plasmid. This plasmid was completely sequenced and revealed a size of 6050 bp. Sequence analyses identified the presence of a resistance gene cluster comprising the genes sul2-ΔstrA-dfrA14-ΔstrA-ΔstrB. Further analysis identified a dfrA14 gene cassette being integrated into the strA reading frame. Neither the gene dfrA14 nor this gene cluster have been detected before in P. multocida.

Carrier flies of multidrug-resistant Escherichia coli as potential dissemination agent in dairy farm environment

The life cycle of synanthropic flies and their behavior, allows them to serve as mechanical vectors of several pathogens. Given that flies can carry multidrug-resistant (MDR) bacteria, this study aimed to investigate the spread of genes of antimicrobial resistance in Escherichia coli isolated from flies collected in two dairy farms in Brazil. Besides antimicrobial resistance determinants, the presence of virulence genes related to bovine colibacillosis was also assessed. Of 94 flies collected, Musca domestica was the most frequently found in the two farms. We isolated 198 E. coli strains (farm A=135 and farm B=63), and >30% were MDR E. coli. We found an association between bla_TEM and phenotypical resistance to ampicillin, or chloramphenicol, or tetracycline; and bla_CTX-M and resistance to cefoperazone. A high frequency (86%) of phylogenetic group B1 among MDR strains and the lack of association between multidrug resistance and virulence factors suggest that antimicrobial resistance possibly is associated with the commensal bacteria. Clonal relatedness of MDR E. coli performed by Pulsed-Field Gel Electrophoresis showed wide genomic diversity. Different flies can carry clones, but with distinct antimicrobial resistance pattern. Sanger sequencing showed that the same class 1 integron arrangement is displayed by apparently unrelated strains, carried by different flies. Our conjugation results indicate class 1 integron transfer associated with tetracycline resistance. We report for the first time, in Brazil, that MDR E. coli is carried by flies in the milking environment. Therefore, flies can act as carriers for MDR strains and contribute to dissemination routes of antimicrobial resistance.

An outbreak of fluoroquinolone-resistant Pseudomonas aeruginosa ST357 harboring the exoU gene

Antimicrobial-resistant isolates of Pseudomonas aeruginosa collected from 2005 to 2014 in a university hospital in Kyoto, Japan, were retrospectively analyzed by multilocus sequence typing (MLST), exoenzyme genotype determination, integron characterization, and clinical associations. During the study, 1573 P. aeruginosa isolates were detected, and 41 of these were resistant to more than two classes of antimicrobial agents. Twenty-five (61.0%) isolates were collected from urine. All isolates were resistant to ciprofloxacin, 8 (19.5%) isolates showed resistance to imipenem/cilastatin, and 8 (19.5%) isolates showed resistance to meropenem. None of the isolates fulfilled the clinical criteria for multidrug-resistant P. aeruginosa. All isolates were negative in the metallo-β lactamase test. Thirty-six (87.8%) isolates were of the exoS^-exoU⁺ genotype and 5 (12.2%) isolates were of the exoS⁺exoU^- genotype. Among 36 exoS^-exoU⁺ isolates, 33 (80.5%) were ST357, and 3 (7.3%) were ST235. Five isolates of exoS⁺exoU^- were ST186, ST244, ST314, ST508, and ST512. Thirty-three isolates were positive for class 1 integrons and four different class 1 integrons were detected: aminoglycoside (2') adenyltransferase and chloramphenicol transporter (AadB+CmlA6), OXA-4 β-lactamase and aminoglycoside 3'-adenyltransferase (OXA4+AadA2), AadB alone, and aminoglycoside acetyltransferase alone (AacA31). Among the 41 patients from which the isolates originated, the most common underlying disease was cancer in 16 patients (39%), and 9 patients (22.0%) died during the hospitalization period. There was no statistical correlation between MLST, exoenzyme genotype, and patient mortality. The results indicated outbreaks of fluoroquinolone-resistant P. aeruginosa in immunocompromised patients mainly due to the propagation of potentially virulent ST357 isolates possessing the exoU⁺ genotype.

Spread of multidrug-resistant Escherichia coli harboring integron via swine farm waste water treatment plant

Wastewater treatment plants (WWTPs) that release treated wastewater into the environment have emerged as a major threat to public health. In this study, we investigated Escherichia coli load and antibiotic-resistance profiles across different treatment processes at a swine farm WWTP. The frequency of the detection of class 1 and 2 integrons, and their association with antibiotic resistance, were also analyzed. Samples were obtained at each of five sampling sites that represented each processing step within the WWTP. The largest decrease in E. coli load was observed during the anaerobic digestion step (from 4.86 to 2.89log CFU/mL). Isolates resistant to β-lactam antibiotics were efficiently removed after a series of treatment steps, whereas the proportions of isolates resistant to non-β-lactam antibiotics and multidrug-resistant strains were maintained across treatments. The occurrence of integron-positive strains was not significantly different at the various sampling sites (43.4-70%; p>0.05). Of the class 1 integron-positive isolates, 17.9% harbored the integron-associated gene cassettes aadA2, aadA12, aadA22, and dfrA15. To the best of our knowledge, this is the first description of a class 1 integron containing the aadA12 gene cassette from a swine farm and the presence of a class 1 integron containing dfrA15 in E. coli. This suggests that novel antibiotic-resistance gene cassette arrays could be generated in swine farm WWTPs. Moreover, 75% of integron-positive strains were categorized as multidrug resistant, whereas only 15.4% of integron-negative strains were multidrug resistant (p<0.05), indicating that integrons may be responsible for mediating resistance in WWTPs. With regard to the occurrence of multidrug-resistant, integron-positive E. coli recovered from the final effluent, our results highlighted the potential risks associated with wastewater discharge from swine farm WWTPs in terms of the spread of antibiotic-resistant bacteria to the aquatic environment.

Genotypic Diversity of Multidrug Resistant Shigella species from Iran

BACKGROUND

In many developing countries, shigellosis is endemic and also occurs in epidemics and treatment of multidrug-resistant (MDR) isolates are important. The aims of this study were to determine the antimicrobial susceptibility, prevalence of class 1 and 2 integrons and the clonal relatedness of isolates.

MATERIALS AND METHODS

Antimicrobial susceptibility tests were performed by disc diffusion method. Polymerase chain reaction (PCR)-sequencing technique was employed for detection and characterization of integrons. The genetic relatedness was evaluated by using enterobacterial repetitive intergenic consensus (ERIC) PCR.

RESULTS

There was a high percentage of resistance to trimethoprim-sulfamethoxazole (TMP/SMX) (93.7%), ampicillin (AMP) (87.3%), streptomycin (STR) (84.5%) and tetracycline (TET) (78.9%). Multidrug resistant phenotype was seen in 95.1% of total isolates. Most common MDR profile was TMP/SMX/STR/AMP resistant pattern. Among the 142 Shigella spp. analyzed in this study, 28 isolates were positive for class 1 integron with two types of gene cassette arrays (dfrA17/aadA5 = 31.7% and dfrA7 = 3.8%). The class 2 integron was more frequently detected among the isolates (94.7%) with dfrA1/sat1/aadA1 (69.4%) and dfrA1/sat1 (30.6%) gene cassettes. ERIC-PCR results showed 6, 5, 4 and 3 main genotypes among S. flexneri, S. sonnei, S. boydii and S. dysenteriae isolates, respectively.

CONCLUSIONS

Our findings revealed that multidrug resistant Shigella species with high prevalence of class 2 integron were very common in Iran. In addition, ERIC-PCR patterns showed limited variety of clones are responsible for shigellosis in the region of the study.

Integron mediated bacterial resistance and virulence on clinical pathogens

Integron was recognized as mobile elements responsible for the emergence and diffusion of antibiotic resistance, virulence and pathogenicity. The existence of resistant integron in pathogens may consequently lead to the increasing number of clinical failures in bacterial mediated diseases, as well as the expenses. In this study, a total of 22 clinical pathogens (including E. faecalis, S. aureus, K. pneumoniae, Enterobacter, P. aeruginosa and Acinetobacter) were subjected to the identification of class 1-class 3 integrons and drug resistant gene cassettes by high flux LAMP method. According to the results, the clinical isolates were screened as carrying class 1 integron with dfrA12-orfF-aadA2 cassette array, class 1 integron with dfrA17-aadA5 cassette array, class 1 integron with aadA2 cassette, class 1 integron with bla_VIM2 cassette, class 1 and class 2 integron with dfrA1-sat1-aadA1 and dfrA12-orfF-aadA2 cassette arrays simultaneously, which was accordantly with the previous data. The optimized high flux LAMP assay was proceeded in water bath at 65 °C for 60 min and determined by naked eye, with the time consumption restricted within 2.5 h. Prior to conventional PCR method, the high flux LAMP assay was demonstrated as a highly-specific and highly-sensitive method. This study offered a valid LAMP method in resistance integrons detection for laboratory use, which was time-saving and easy-determination.

Characterization and Horizontal Transfer of Antimicrobial Resistance Genes and Integrons in Bacteria Isolated from Cooked Meat Products in China

The aim of this study was to investigate antimicrobial resistance and the presence and transferability of corresponding resistance genes and integrons in bacteria isolated from cooked meat samples in the People's Republic of China. A total of 150 isolates (22 species belonging to 15 genera) were isolated from 49 samples. Resistance of these isolates to antimicrobials was commonly observed; 42.7, 36.0, and 25.3% of the isolates were resistant to tetracycline, streptomycin, and ampicillin, respectively. Multidrug resistance was observed in 41 (27.3%) of the isolates. Sixteen resistance genes, i.e., bla_TEM-1 and bla_CTX-M-14 (β-lactams), aac(3)-IIa (gentamicin), strA and strB (streptomycin), qnrB and qnrS (fluoroquinolone), sul1, sul2, and sul3 (sulfamethoxazole), cat1 and cat2 (chloramphenicol), and tetM, tetA, tetS, and tetB (tetracycline), were found in 54 isolates. One isolate of Pseudomonas putida carried qnrB, and sequence analysis of the PCR product revealed 96% identity to qnrB2. The qnr genes were found coresiding and were cotransferred with bla genes in two isolates. Twelve isolates were positive for the class 1 integrase gene, and four isolates carried the class 2 integrase gene. However, no class 3 integrase gene was detected. One isolate of Proteus mirabilis carried dfrA32-ereA-aadA2, and this unusual array could be transferred to Escherichia coli. Nonclassic class 1 integrons lacking qacEΔ1 and sul1 genes were found in 2 of the 12 intI1-positive isolates. Our results revealed the presence of multidrug-resistant bacteria in cooked meats and the presence and transferability of resistance genes in some isolates, suggesting that cooked meat products may act as reservoirs of drug-resistant bacteria and may facilitate the spread of resistance genes.

A Highly Promiscuous Integron, Plasmids, Extended Spectrum Beta Lactamases and Efflux Pumps as Factors Governing Multidrug Resistance in a Highly Drug Resistant Vibrio fluvialis Isolate BD146 from Kolkata, India

In an earlier study from this laboratory, Vibrio fluvialis BD146, a clinical isolate from Kolkata, India, 2002, was found to be resistant to all the fourteen antibiotics tested. It harboured a high copy number plasmid pBD146 and a low copy number plasmid. In the present study, a more detailed analysis was carried out to unravel different resistance mechanisms in this isolate. Sequencing showed that variable region of class 1 integron located on low copy number plasmid harbored arr3-cmlA-bla_OXA10-aadA1 gene cassettes. Analysis for extended spectrum beta lactamases (ESBLs) revealed that BD146 was ESBL positive. Efflux pumps were involved in the drug resistance phenotype for chloramphenicol, kanamycin, streptomycin and tetracycline. Sequence analysis of pBD146 revealed the presence of genes encoding BDint an integrase with a unique sequence having little similarity to other known integrases, toxin-antitoxin (parE/parD), a replicase, trimethoprim resistance (dfrVI) and quinolone resistance (qnrVC5). Presence of cmlA, putative novel integrase and toxin-antitoxin system in V. fluvialis has been documented for the first time in this report. pBD146 showed 99% sequence similarity with pVN84 from V. cholerae O1 of Vietnam, 2004 and a plasmid from V. parahaemolyticus v110 of Hong Kong, 2010. Conjugation experiments proved the ability of pBD146 and the low copy number plasmid, to get transferred to another host imparting their antibiotic resistance traits to the transconjugants. Therefore, present study has indicated that plasmids played an important role for dissemination of drug resistance.

Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

BACKGROUND

The global incidence of foodborne infections and antibiotic resistance is recently increased and considered of public health concern. Currently, scarcely information is available on foodborne infections and ESBL associated with poultry and beef meat in Egypt.

METHODS

In total, 180 chicken and beef meat samples as well as internal organs were collected from different districts in northern Egypt. The samples were investigated for the prevalence and antibiotic resistance of Salmonella enterica serovars and Escherichia coli. All isolates were investigated for harbouring class 1 and class 2 integrons.

RESULTS

Out of 180 investigated samples 15 S. enterica (8.3%) and 21 E. coli (11.7%) were isolated and identified. S. enterica isolates were typed as 9 S. Typhimurium (60.0%), 3 S. Paratyphi A (20.0%), 2 S. Enteritidis (13.3%) and 1 S. Kentucky (6.7%). Twenty-one E. coli isolates were serotyped into O1, O18, O20, O78, O103, O119, O126, O145, O146 and O158. The phenotypic antibiotic resistance profiles of S. enterica serovars to ampicillin, cefotaxime, cefpodoxime, trimethoprim/sulphamethoxazole and tetracycline were 86.7, 80.0, 60.0, 53.3 and 40.0%, respectively. Isolated E. coli were resistant to tetracycline (80.9%), ampicillin (71.4%), streptomycin, trimethoprim/sulphamethoxazole (61.9% for each) and cefotaxime (33.3%). The dissemination of genes coding for ESBL and AmpC β-lactamase in S. enterica isolates included bla_CTX-M (73.3%), bla_TEM (73.3%) and bla_CMY (13.3%). In E. coli isolates bla_TEM, bla_CTX-M and bla_OXA were identified in 52.4, 42.9 and 14.3%, respectively. The plasmid-mediated quinolone resistance genes identified in S. enterica were qnrA (33.3%), qnrB (20.0%) and qnrS (6.7%) while qnrA and qnrB were detected in 33.3% of E. coli isolates. Class 1 integron was detected in 13.3% of S. enterica and in 14.3% of E. coli isolates. Class 2 integron as well as the colistin resistance gene mcr-1 was not found in any of E. coli or S. enterica isolates.

CONCLUSIONS

This study showed high prevalence of S. enterica and E. coli as foodborne pathogens in raw chicken and beef meat in Nile Delta, Egypt. The emergence of antimicrobial resistance in S. enterica and E. coli isolates is of public health concern in Egypt. Molecular biological investigation elucidated the presence of genes associated with antibiotic resistance as well as class 1 integron in S. enterica and E. coli.

Emergence of class 1 to 3 integrons among members of Enterobacteriaceae in Egypt

In spite of the role of integrons as the main contributor to multidrug resistance worldwide, their prevalence in Egypt is still underestimated. In this work, we announce the emergence of class 2 and 3 integrons among Enterobacteriacae isolates from Mansoura University Hospitals. Ninety-three clinical isolates were obtained from different clinical sources, among which 70% of E. coli, 94.8% of K. pneumoniae and 85.7% of Enterobacter spp. were assigned to be multidrug resistant (MDR). Subsequently, the occurrence of class 1-3 integrons was confirmed by multiplex PCR. Class 1 integron was the most predominant being harbored by 42.8%, 90% and 25% of MDR E. coli, K. pneumoniae and Enterobacter spp. isolates, respectively. This was followed by class 2 and 3 integrons which were, for the first time, reported in these hospitals. Also, coexistence of integrons 1and 2 was revealed in 36.9% of integron positive isolates. A significant association was noticed only between resistance to gentamicin and integron prevalence among MDR E. coli isolates (P = 0.02). In conclusion, this work represents the first report for detection of class 2 and 3 integrons, beside the previously detected class 1 integrons. This highlights the high incidence of integrons among MDR Enterobacteriacae isolates which indicates the selective pressure of antibiotics in these hospitals. Moreover, this study confirms the possibility of the use of integrons as markers for MDR identification.

Study on the excision and integration mediated by class 1 integron in Streptococcus pneumoniae

As a novel antibiotic resistance mobile element, integron was recognized as a primary source of antibiotic genes among Gram-positive organisms for its excision and integration of exogenous genes. In this study, Streptococcus pneumoniae was subjected to investigate the excision and integration of class 1 integron with eight different plasmids. As the results indicated, excision in both att site and gene cassettes were successfully observed, which was further confirmed by integration assays and PCR amplification. The observation of class 1 integron mediated excision and integration of various exogenous antibiotics resistance genes may raise the attention of integrons as novel antibiotic resistance determinant in Gram-positive bacteria, especially in Streptococcus.

Microbial pathogenicity and virulence mediated by integrons on Gram-positive microorganisms

Gram-positive microorganisms are one of leading pathogenic microorganisms in public health, including several typical "Super Bugs" as methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae carbapenemase and vancomycin-resistant enterococci, which caused a increasement of infections, clinical failures and expenses. Regarded as a common genetic element responsible for horizontal gene transfer, integrons are widely distributed in various pathogens considered as a determinant in the acquisition and evolution of antibiotic resistance. Current investigations mainly focus on the distribution of integrons in Gram-negative microorganisms, while the role of integron in antibiotic resistance among Gram-positive microorganisms remains unclear and need investigation. To date, the surveillances of integrons in Gram-positive microorganism have been widely conducted in clinic, community even husbandry. China remains one of the worst country in antibiotics abuse worldwide and considered as a potential area for the prevalence of antimicrobial microorganisms and the occurrence of various 'Super Bugs'. Recently, the surveillance of the occurrence of integron and resistance gene cassettes was conducted in South China during the first 10 years of the 21st century. Referred to the surveillance in South China and other investigation in Asian countries, this review aims to summarize the occurrence, pathogenicity and virulence mediated by integrons in typical Gram-positive microorganisms (Staphylococcus, Enterococcus, Corynebacterium and Streptococcus) and the role of integrons in antibiotic resistance.

Transmission and characterization of bla NDM-1 in Enterobacter cloacae at a teaching hospital in Yunnan, China

Background

In recent years, New Delhi metallo-beta-lactamases 1 (bla_NDM-1) has been reported with increasing frequency and become prevalent. The present study was undertaken to investigate the epidemiological dissemination of the bla_NDM-1 gene in Enterobacter cloacae isolates at a teaching hospital in Yunnan, China.

Methods

Antimicrobial susceptibility testing was performed using VITEK 2 system and E test gradient strips. The presence of integrons and insertion sequence common region 1 were examined by PCR and sequencing. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Conjugation experiments and Southern blot hybridization were performed to determine the transferability of plasmids.

Results

Ten E. cloacae isolates and their Escherichia coli transconjugants were exhibited similar resistant patterns to carbapenems, cephalosporins and penicillins. 8 (80%) of E. cloacae isolates carried class 1 integron and 1 (12.5%) carried class 2 integron. Integron variable regions harbored the genes which encoded resistance to aminoglycosides (aadA1, aadA2, aadA5, aadB, aac(6′)-Ib-cr), sulfamethoxazole/trimethoprim (dfrA17, dfrA12, dfrA15) and Streptozotocin (sat2). Six E. cloacae isolates belonged to ST74 and exhibited highly similar PFGE patterns. Each isolate shared an identical plasmid with ~33.3 kb size that carried the bla_NDM-1 gene, except T3 strain, of which the bla_NDM-1 gene was located on a ~50 kb plasmid.

Conclusions

Our findings suggested that plasmid was able to contribute to the dissemination of bla_NDM-1. Hence, more attention should be devoted to monitor the dissemination of the bla_NDM-1 gene due to its horizontal transfer via plasmid. In addition, nosocomial surveillance system should actively monitor the potential endemic clone of ST74 to prevent their further spread.

Does antifouling paint select for antibiotic resistance?

There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.

A 10-year surveillance of antimicrobial susceptibility patterns in Shigella sonnei isolates circulating in Jiangsu Province, China

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Long-term multicentre surveillance of antimicrobial susceptibility patterns in Shigella sonnei.

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Epidemic clones and integron types and resistance gene cassettes were characterised.

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PFGE indicated large-scale clonal transmission among different cities occurred several times during 10 years.

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Class 1, 2 and atypical class 1 integrons were detected in S. sonnei.

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High prevalence of integrons and gene cassettes was related to the increasing antimicrobial resistance.

Objectives

The rapid emergence of drug-resistant Shigella sonnei is a serious public health problem. This study aimed to characterise the antimicrobial resistance patterns, molecular subtypes, and integron types and resistance gene cassettes in S. sonnei from Jiangsu Province, China.

Methods

In total, 340 S. sonnei were collected in 2002–2011 throughout Jiangsu Province. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), PCR amplification of integrons, restriction fragment length polymorphism (RFLP) and DNA sequencing of cassette regions were performed.

Results

Resistance rates to ampicillin (67.7%), nalidixic acid (75.2%), tetracycline (73.7%) and trimethoprim/sulfamethoxazole (68.7%) remained high. Strains from Centre and South Jiangsu showed higher resistance and multiresistance rates compared with the North. PFGE analysis indicated that large-scale clonal transmission among different cities occurred several times during 10 years. Among all strains, 55.9% (190/340) harboured class 1 integrons, 80.3% (273/340) harboured class 2 integrons and 49.4% (168/340) harboured an atypical class 1 integron. Resistance rates to nine antimicrobials in the class 1 integron-positive group were significantly higher than in the negative group (P < 0.05). Seven different gene cassettes were detected in class 1 integrons. The most prevalent type was aacA4–cmlA1 (114/286). Class 2 integrons carried the gene cassette array dfrA1–sat1–aadA1, and the atypical class 1 integron carried bla_OXA-30–aadA1.

Conclusions

The increasing antimicrobial resistance and significant clonal transmission of S. sonnei circulating in Jiangsu were closely related to the high prevalence of integrons and gene cassettes. Long-term cross-regional monitoring of antimicrobial resistance is urgently required for S. sonnei.

Integron types, gene cassettes and antimicrobial resistance profile of Acinetobacter baumannii isolated from BAL samples in Babol, north of Iran

Multi-drug resistant isolates of Acinetobacter baumannii have created therapeutic problems worldwide. This current study was intended to determine the Integron types, gene cassettes and antimicrobial resistance profile of A. baumannii isolated from BAL samples in Babol, north of Iran. During a 15-month period, 35 A. baumannii isolates were studied. Different classes of antimicrobial agents were used to determine the resistance ratios. Multiplex-PCR was used to detect different types of integrons and associated gene cassettes. The resistance rates to GM, FEP, AK, TOB, CP, PIP, SAM, IPM, SXT, CTX, CAZ, CL, TIM, MEM, and TZP were 85.7%, 100%, 91.4%, 68.5%, 94.3%, 88.5%, 97.1%, 94.3%, 100%, 100%, 100%, 0.0%, 91.4%, 94.3% and 91.4%, respectively. The distribution analysis of int genes showed that 25.7%, 88.6% and 28.6% of isolates carried the intI, intII and intIII genes, respectively. The prevalence of aadB, dfrA1, bla-OXA₃₀ and aadA1 genes were 94.3%, 77.1%, 40% and 5.7%, respectively. The current study showed that a high level of A. baumannii isolates harbor integrons in our therapeutic center, which may lead to distribution of multiple antimicrobial resistance. The different types of gene cassette arrays in the present study highlight the important role of geographical features in MDR isolates dissemination which could be credited to different profiles of drug consumption in different areas. The findings emphasized that the need for continuous surveillance to prevent distribution of multidrug resistance among A. baumannii strains in Iran.

Expansion of highly stable bla OXA-10 β-lactamase family within diverse host range among nosocomial isolates of Gram-negative bacilli within a tertiary referral hospital of Northeast India

Background

The current study reports dissemination of highly stable bla_OXA-10 family of beta lactamases among diverse group of nosocomial isolates of Gram-negative bacilli within a tertiary referral hospital of the northern part of India.

Methods

In the current study, a total number of 590 Gram negative isolates were selected for a period of 1 year (i.e. 1st November 2011–31st October 2012). Members of Enterobacteriaceae and non fermenting Gram negative rods were obtained from Silchar Medical College and Hospital, Silchar, India. Screening and molecular characterization of β-lactamase genes was done. Integrase gene PCR was performed for detection and characterization of integrons and cassette PCR was performed for study of the variable regions of integron gene cassettes carrying bla_OXA-10. Gene transferability, stability and replicon typing was also carried out. Isolates were typed by ERIC as well as REP PCR.

Results

Twenty-four isolates of Gram-negative bacilli that were harboring bla_OXA-10 family (OXA-14, and OXA16) with fact that resistance was to the extended cephalosporins. The resistance determinant was located within class I integron in five diverse genetic contexts and horizontally transferable in Enterobacteriaceae, was carried through IncY type plasmid. MIC values were above break point for all the tested cephalosporins. Furthermore, co-carriage of bla_CMY-2 was also observed.

Conclusion

Multiple genetic environment of bla_OXA-10 in this geographical region must be investigated to prevent dissemination of these gene cassettes within bacterial population within hospital settings.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-017-2467-2) contains supplementary material, which is available to authorized users.

Occurrence of a novel class 1 integron harboring qnrVC4 in Salmonella Rissen

We described qnrVC4 in S. Rissen 166ANSS50, a swine isolate, which was detected in the study on quinolone resistance mechanisms of nontyphoidal Salmonella in Thailand. The isolate was found to harbor a ̴17-kb non-conjugative plasmid carrying qnrVC4 within 8.91kb of a novel In4-like class 1 integron (In805). It contained the multi-drug resistance gene cassettes of qnrVC4-qacH4-aacA4-cmlA7-bla_OXA-10-aadA1-dfrA14 and unusual 3'-CS of mobC-IS6100. This 1014-bp qnrVC4 cassette included with promoter (P_qnrVC4: -35 TTGAGA and -10 TAGTCT) showed high homology with qnrVC4 in superintegron of V. cholerae O1 El Tor. The qnrVC4 recombinant plasmid resulted in 4-, 8-, and 16-fold increase in the MICs of nalidixic acid (2-8μg/mL), ciprofloxacin (0.015-0.125μg/mL), and norfloxacin (0.03-0.5μg/mL), respectively. In addition, the backbone plasmid revealed a novel replicon belonging to the MOB_Q1 group from the broad-host-range mobilisable IncQ1 plasmid RFS1010 based on relaxase sequences. This is the first known report of qnrVC in Salmonella enterica. The qnrVC4 gene was co-transferred with other resistance genes via a novel plasmid-borne In805. This allowed the spread of this resistance gene to Enterobacteriaceae.