Defining the Relationship Between Phenotypic and Genotypic Resistance Profiles of Multidrug-Resistant Enterobacterial Clinical Isolates

Multiple sequence types, virulence determinants and antimicrobial resistance genes in multidrug- and colistin-resistant Escherichia coli from agricultural and non-agricultural soils

In soils, the presence of clinically relevant bacteria carrying ARGs, including extended-spectrum β-lactamase- and plasmid-mediated AmpC β-lactamase-encoding genes, is an underestimated public health problem that requires more attention. For this investigation, 300 samples from agricultural and non-agricultural soils were used to obtain 41 MDR E. coli isolates, standing out the resistance to β-lactams, fluoroquinolones and colistin. Virulence genes related to diarrheagenic E. coli and extraintestinal pathogenic E. coli were detected. Several ARGs were found, highlighting the presence of at least one β-lactamase-encoding gene (bla_TEM, bla_CMY, bla_SHV, bla_OXA-1-like, bla_CTX-M-2, and/or bla_CTX-M-15) in each isolate. Among the fluoroquinolone-resistant E. coli isolates, the plasmid-mediated quinolone resistance genes (qnrB and oqxA) and substitutions in the quinolone resistance-determining regions were detected. Some isolates were resistant to colistin (MICs of 4-8 mg/L) and, although no mcr-like gene was detected, substitutions in the two-component systems involving PhoP/PhoQ and PmrA/PmrB were found. Furthermore, the E. coli isolates presented plasmids and class 1 integrons, the last one detected in all isolates. The ARGs bla_TEM, aadA and dfrA and the lpfA virulence-associated gene presented statistically significant differences (P < 0.05) in agricultural soils, while the bla_OXA-1-like gene presented a statistically significant difference in non-agricultural soils. Thirty-eight sequence types (STs) were identified among the isolates, spotlighting the 20 different STs that carried bla_CMY and bla_CTX-M-type genes and those commonly reported in infections worldwide. The occurrence of virulent, multidrug- and colistin-resistant E. coli isolates in soils could lead to contamination of surrounding environments and food, increasing the risk of human and animal exposure. Therefore, this study contributes to a better understanding of E. coli in soils and reinforces the importance of the One Health approach to antimicrobial resistance surveillance.

Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal

The emergence and dissemination of resistance to third- and fourth-generation cephalosporins among Enterobacteriaceae from different sources impose a global public health threat. Here, we characterized by whole-genome sequencing four Escherichia coli strains harboring the bla_CTX–M–65 gene identified among 49 isolates from beef and pork collected at retail. The genomic content was determined using the Center for Genomic Epidemiology web tools. Additionally, the prediction and reconstruction of plasmids were conducted, the genetic platform of the bla_CTX–M–65 genes was investigated, and phylogenetic analysis was carried out using 17 other genomes with the same sequence type and harboring the bla_CTX–M–65 gene. All strains harbored bla_CTX–M–65, bla_OXA–1, and bla_TEM–1B, and one also carried the bla_SHV–12 gene. Other resistance genes, namely, qnrS2, aac(6′)-Ib-c, dfrA14, sul2, tetA, and mphA, were present in all the genomes; the mcr-1.1 gene was identified in the colistin-resistant strains. They belong to sequence type 2179, phylogenetic group B1, and serotype O9:H9 and carried plasmids IncI, IncFIC(FII), and IncFIB. All strains share an identical genetic environment with IS903 and ISEcp1 flanking the bla_CTX–M–65 gene. It seems likely that the bla_CTX–M–65 gene is located in the chromosome in all isolates based on deep in silico analysis. Our findings showed that the strains are clonally related and belong to two sub-lineages. This study reports the emergence of CTX-M-65-producing E. coli in Portugal in food products of animal origin. The chromosomal location of the bla_CTX–M–65 gene may ensure a stable spread of resistance in the absence of selective pressure.

Landscape of Multidrug-Resistant Gram-Negative Infections in Egypt: Survey and Literature Review

Purpose

This article is the first to review published reports on the prevalence of multidrug-resistant (MDR) gram-negative infections in Egypt and gain insights into antimicrobial resistance (AMR) surveillance and susceptibility testing capabilities of Egyptian medical centers.

Materials and Methods

A literature review and online survey were conducted.

Results

The online survey and literature review reported high prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (19–85.24% of E. coli, and 10–87% of K. pneumoniae), carbapenem-resistant Enterobacteriaceae (35–100% of K. pneumoniae and 13.8–100% of E. coli), carbapenem-resistant Acinetobacter baumannii (10–100%), and carbapenem-resistant Pseudomonas aeruginosa (15–70%) in Egypt. Risk factors for MDR Gram-negative infections were ventilated patients (67.4%), prolonged hospitalization (53.5%) and chronic disease (34.9%). Although antimicrobial surveillance capabilities were deemed at least moderate in most centers, lack of access to rapid AMR diagnostics, lack of use of local epidemiological data in treatment decision-making, lack of antimicrobial stewardship (AMS) programs, and lack of risk prediction tools were commonly reported by respondents.

Conclusion

This survey has highlighted the presence of knowledge gaps as well as limitations in the surveillance and monitoring capabilities of AMR in Egypt, with most laboratories lacking rapid diagnostics and molecular testing. Future efforts in Egypt should focus on tackling these issues via nationwide initiatives, including understanding the AMR trends in the country, capacity building of laboratories and their staff to correctly and timely identify AMR, and introducing newer antimicrobials for targeting emerging resistance mechanisms in Gram-negative species.

Genetic characterization of clinical <I>Klebsiella</I> isolates circulating in Novosibirsk

Проанализированы 72 клинических штамма Klebsiella spp., изолированных в Новосибирске из образцов, полученных от людей. Проведена видовая идентификация штаммов по последовательностям генов 16S рРНК и rpoB. Показано, что в популяции клебсиелл доминировали штаммы Klebsiella pneumoniaе (57 штаммов), остальные 15 штаммов относились к видам K. grimontii, K. aerogenes, K. oxytoca и K. quasipneumoniae. Методом молекулярного серотипирования с использованием последовательности гена wzi штаммы K. pneumoniae были отнесены к двадцати одному K-cеротипу, при этом большую долю составляли вирулентные серотипы K1 и K2. Выявлено, что штаммы K. pneumoniae, полученные от госпитализированных пациентов, обладали максимально выраженной резистентностью к различным классам антибиотиков в отличие от остальных видов клебсиелл. Методом ПЦР в реальном времени обнаружено, что в исследованной популяции присутствуют гены семейств blaSHV, blaTEM, blaCTX и ген blaOXA-48 , являющиеся генетическими детерминантами резистентности к бета-лактамам. Показано, что присутствие последовательности blaCTX коррелирует с продукцией штаммом бета-лактамаз расширенного спектра, а фенотипическая устойчивость к карбапенемам обусловлена наличием гена blaOXA-48 . При этом генов карбапенемаз vim, ndm, kpc, imp обнаружено не было. Cреди исследованных генов устойчивости к аминогликозидам были найдены гены aph(6)-Id и aadA, однако их наличие не всегда совпадало с фенотипической резистентностью. Устойчивость к фторхинолонам у большинства штаммов сопровождалась присутствием генов aac(6’)-Ib-cr, oqxA, oqxB, qnrB и qnrS в различных комбинациях, при этом наличие только генов oqxA и/или oqxB не коррелировало с устойчивостью к фторхинолонам. Таким образом, обнаружение blaCTX и blaOXA-48 может быть использовано для быстрого выявления продукции беталактамаз расширенного спектра и определения резистентности клебсиелл к карбапенемам, а выявление генов aac(6’)-Ib-cr и/или qnrB/qnrS – для быстрого определения устойчивости к фторхинолонам

Plasmid-mediated quinolone resistance: Mechanisms, detection, and epidemiology in the Arab countries

Quinolones are an important antimicrobial class used widely in the treatment of enterobacterial infections. Although there are multiple mechanisms of quinolone resistance, attention should be paid to plasmid-mediated genes due to their ability to facilitate the spread of quinolone resistance, the selection of mutants with a higher-level of quinolone resistance, and the promotion of treatment failure. Since their discovery in 1998, plasmid-mediated quinolone resistance (PMQR) mechanisms have been reported more frequently worldwide especially with the extensive use of quinolones in humans and animals. Nevertheless, data from the Arab countries are rare and often scattered. Understanding the prevalence and distribution of PMQR is essential to stop the irrational use of quinolone in these countries. This manuscript describes the quinolone resistance mechanisms and particularly PMQR among Enterobacteriaceae as well as their methods of detection. Then the available data on the epidemiology of PMQR in clinical and environmental isolates from the Arab countries are extensively reviewed along with the other associated resistance genes. These data shows a wide dissemination of PMQR genes among Enterobacteriaceae isolates from humans, animals, and environments in these countries with increasing rates over the years and a common association with other antibiotic resistance genes as bla_CTX-M-15. The incontrovertible emergence of PMQR in the Arab countries highlights the pressing need for effective stewardship efforts to prevent the selection of a higher rate of quinolone resistance and to preserve these crucial antibiotics.

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.