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

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Characterization of Integrons and Quinolone Resistance in Clinical Escherichia coli Isolates in Mansoura City, Egypt

Escherichia coli is a common pathogen in both humans and animals. Quinolones are used to treat infections caused by Gram-negative bacteria, but resistance genes emerged. Only scarce studies investigated the association between plasmid-mediated quinolone resistance (PMQR) genes and integrons in clinical isolates of E. coli. The current study investigated the prevalence of quinolone resistance and integrons among 134 clinical E. coli isolates. Eighty (59.70%) isolates were quinolone-resistant, and 60/134 (44.77%) isolates were integron positive with the predominance of class I integrons (98.33%). There was a significant association between quinolone resistance and the presence of integrons (P < 0.0001). Isolates from Urology and Nephrology Center and Gastroenterology Hospital were significantly quinolone-resistant and integron positive (P ≤ 0.0005). Detection of PMQR genes on plasmids of integron-positive isolates showed that the active efflux pump genes oqxAB and qepA had the highest prevalence (72.22%), followed by the aminoglycoside acetyltransferase gene (aac(6′)-Ib-cr, 66.67%) and the quinolone resistance genes (qnr, 61.11%). Amplification and sequencing of integrons' variable regions illustrated that no quinolone resistance genes were detected, and the most predominant gene cassettes were for trimethoprim and aminoglycoside resistance including dfrA17, dfrB4, and dfrA17-aadA5. In conclusion, this study reported the high prevalence of PMQR genes and integrons among clinical E. coli isolates. Although PMQR genes are not cassette-born, they were associated with integrons' presence, which contributes to the widespread of quinolone resistance in Egypt.

Integron-Related Resistance in New Emerged Staphylococcus lugdunensis Infection in Burn Patients

Staphylococcus lugdunensis is a coagulase-negative Staphylococcus species that may cause various infections with unusual severity. In spite of the administration of various antibiotics, infections caused by such bacteria are become resistant significantly. Transmission of antibiotic resistance genes, especially by Integron structures, exacerbates the prevalence of resistant strains. To investigate the antibiotic susceptibility pattern of S. lugdunensis as a new emergence in burns, the presence of integron classes (I, II, III) was performed in recent study. Sampling for this study was carried out over a period of 13 months (January 2017 to February 2018) from Amir-Al-Momenin burn center of southwest of Iran, affiliated with Shiraz University of Medical Sciences. Twenty-eight isolates of S. lugdunensis were confirmed by phenotypic tests. The presence of integron classes was evaluated by PCR technique and specific primers. The majority of studied infectious agents were seen in ICU with 28.57%. The prevalence of class I and II integrons was 7 (25.00%) and 2 (7.14%), respectively, in S. lugdunensis isolates, whereas no integron III was found. No significant association was seen between antibiotic resistance and the present integrons (P > .05). Since the prevalence of S. lugdunensis strains as a new emergence infection is increasing in clinical settings especially burns, preventing drug resistance in these isolates is inevitable. So knowing the epidemiology pattern of new emerging infections and their resistant pattern is very helpful in infection control and save hospitalized patients life.

Characterization of β-lactam resistance in K. pneumoniae associated with ready-to-eat processed meat in Egypt

K. pneumoniae was known as a nosocomial infection that causes human diseases. It is considered as one of the food-borne pathogens as it causes septicemia and diarrhea in humans. This study aims to characterize K. pneumoniae strains isolated from ready to eat processed meat phenotypically and genetically. Three hundred and fifty ready to eat processed meat (Luncheon-meat) samples were collected. Forty-four (12.6%) K. pneumoniae strains were isolated and bio-typed, where the majority were identified to belong to biotype B1. K1 and K2 serotypes were detected and strains were classified as hypermucoviscous K. pneumoniae (HVKP) and classic K. pneumoniae (CKP) (26 and 18 isolates, respectively). The isolates were resistant to several classes of β–lactam antibiotics, ceftazidim and cefotaxime (95.5%), cefoxitin (93.2%), ertapenem (90.9%) and amoxicillin-clavulanic acid (86.4%). They were classified as extended spectrum β–lactamases (ESBLs), AmpC or carbapenemase-producers phenotypically. Eighteen β-lactamase genes were investigated by PCR. The most prominent genes were SHV (63.6%), TEM (52.2%), CTX-M15 (50%), AMPC (47.7%), CIT-M (45.5%) and VIM (43.2%). Co-detection of β–lactam resistance genes revealed 42 gene profiles. Twenty-four isolates had the complete efflux system (AcrAB-ToƖC). Besides, Integrons (I, II, III) were detected in 20 isolates. Molecular typing by ERIC-PCR showed high genetic diversity between isolates as 34 different patterns were identified. Overall, this study confirmed the hazards posed by the presence of multiple resistance genes in the same isolate and this should not be undervalued. Besides, the horizontal transfer of plasmid harboring resistance genes between isolates in food represents potential health risks for consumers in Egypt and so the control and inhibition plans are necessary.

The complex genetic region conferring transferable antibiotic resistance in multidrug-resistant and extremely drug-resistant Klebsiella pneumoniae clinical isolates

Antibiotic resistance due to transferable resistance genes is one of the most important concerns in Klebsiella pneumoniae isolated from nosocomial infections. Eighty-eight K. pneumoniae isolates were confirmed through biochemical methods. In addition, antimicrobial susceptibility testing was performed using a disc-diffusion method. Extended-spectrum β-lactamase production among the isolates was screened using a double-disc synergism test, and the resistance genes were identified using PCR. The eight loci for multiple-locus variable number tandem repeat analysis (MLVA) genotyping were selected along with the primers. According to our findings, neomycin (5; 5.6%) and carbapenems (10; 11.3%) showed the most remarkable inhibitory effect but co-trimoxazole (46; 52.2%) was the least effective antibiotic against K. pneumoniae isolates. bla _CTX-M-1 , qnrA, qnrB, qnrS, intI, intII, aac3 and aac6 were detected in 30 (34%), 5 (5.6%), 29 (32.9%), 23 (26.1%), 88 (100%), 72 (81.8%), 26 (29.5%) and 28 (31.8%) of the 88 isolates, respectively. But none of the K. pneumoniae isolates expressed the intIII gene. Using MLVA, 23 MLVA types and eight clusters were identified. Extended-spectrum β-lactamase-producing K. pneumoniae isolates were classified into two clonal complexes. Effective strategies for infection control should be applied to monitor and control the spread of multidrug-resistant isolates by the resistance genes located on the mobile genetic elements.

Prevalence of Integrons and Insertion Sequences in ESBL-Producing E. coli Isolated from Different Sources in Navarra, Spain

Mobile genetic elements play an important role in the dissemination of antibiotic resistant bacteria among human and environmental sources. Therefore, the aim of this study was to determine the occurrence and patterns of integrons and insertion sequences of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from different sources in Navarra, northern Spain. A total of 150 isolates coming from food products, farms and feeds, aquatic environments, and humans (healthy people and hospital inpatients), were analyzed. PCRs were applied for the study of class 1, 2, and 3 integrons (intI1, intI2, and intI3), as well as for the determination of insertion sequences (IS26, ISEcp1, ISCR1, and IS903). Results show the wide presence and dissemination of intI1 (92%), while intI3 was not detected. It is remarkable, the prevalence of intI2 among food isolates, as well as the co-existence of class 1 and class 2 (8% of isolates). The majority of isolates have two or three IS elements, with the most common being IS26 (99.4%). The genetic pattern IS26⁻ISEcp1 (related with the pathogen clone ST131) was present in the 22% of isolates (including human isolates). In addition, the combination ISEcp1⁻IS26⁻IS903⁻ISCR1 was detected in 11 isolates being, to our knowledge, the first study that describes this genetic complex. Due to the wide variability observed, no relationship was determined among these mobile genetic elements and β-lactam resistance. More investigations regarding the genetic composition of these elements are needed to understand the role of multiple types of integrons and insertion sequences on the dissemination of antimicrobial resistance genes among different environments.

Epidemiology of common resistant bacterial pathogens in the countries of the Arab League

No uniformly organised collection of data regarding antimicrobial resistance has occurred in the countries of the Arab League. 19 countries of the Arab League have published data for antimicrobial susceptibility for the WHO priority organisms, and seven of 14 of these organisms are included in this Review (Escherichia coli, Klebsiella spp, Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella spp, Staphylococcus aureus, and Streptococcus pneumoniae). Although E coli and Klebsiella spp resistance to third-generation cephalosporins is common in all countries, with prevalence reaching more than 50% in Egypt and Syria, carbapenem resistance is emerging, albeit with a prevalence of less than 10%. Conversely, a large amount of carbapenem resistance has been reported for P aeruginosa and A baumannii across the Arab League, reaching 50% and 88% of isolates in some countries. As for Salmonella spp, the prevalence of fluoroquinolone resistance has exceeded 30% in several areas. With regards to the Gram-positive pathogens, the prevalence of meticillin resistance in S aureus is reported to be between 20% and 30% in most countries, but exceeds 60% in Egypt and Iraq. The prevalence of penicillin non-susceptibility among pneumococci has reached more than 20% in Algeria, Egypt, Morocco, Saudi Arabia, and Tunisia. These findings highlight the need for structured national plans in the region to target infection prevention and antimicrobial stewardship.