Genetic characterisation of CTX-M-15-producing Klebsiella pneumoniae and Escherichia coli strains isolated from stem cell transplant patients in Tunisia

Molecular characterization and prevalence of β-lactamase-producing Enterobacterales in livestock and poultry slaughterhouses wastewater in Iran

Beta-lactamase-producing Enterobacterales bacteria cause severe hard-to-treat infections. Currently, they are spreading beyond hospitals and becoming a serious global health concern. This study investigated the prevalence and molecular characterization of extended-spectrum β-lactamase and AmpC-type β-lactamase-producing Enterobacterales (ESBL-PE, AmpC-PE) in wastewater from livestock and poultry slaughterhouses in Ardabil, Iran. A total of 80 Enterobacterales bacteria belonging to 9 species were identified. Among the isolates, Escherichia coli (n = 21/80; 26.2%) and Citrobacter spp. (n = 18/80; 22.5%) exhibited the highest frequency. Overall, 18.7% (n = 15/80) and 2.5% (n = 2/80) of Enterobacterales were found to be ESBL and AmpC producers, respectively. The most common ESBL producer isolates were E. coli (n = 9/21; 42.8%) and Klebsiella pneumoniae (n = 6/7; 85.7%). All AmpC-PE isolates belonged to E. coli strains (n = 2/21; 9.5%). In this study, 80% of ESBL-PE and 100% of AmpC-PE isolates were recovered from poultry slaughterhouse wastewater. All ESBL-PE and AmpC-PE isolates were multidrug-resistant. In total, 93.3% of ESBL-PE isolates harbored the blaCTX-M gene, with the blaCTX-M-15 being the most common subgroup. The emergence of ESBL-PE and AmpC-PE in wastewater of food-producing animals allows for zoonotic transmission to humans through contaminated food products and contaminations of the environment.

Occurrence of High-Risk Clonal Lineages ST58, ST69, ST224, and ST410 among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Free-Range Chickens (Gallus gallus domesticus) in a Rural Region in Tunisia

Antimicrobial-resistant Escherichia coli isolates have emerged in various ecologic compartments and evolved to spread globally. We sought to (1.) investigate the occurrence of ESBL-producing E. coli (ESBL-Ec) in feces from free-range chickens in a rural region and (2.) characterize the genetic background of antimicrobial resistance and the genetic relatedness of collected isolates. Ninety-five feces swabs from free-range chickens associated with two households (House 1/House 2) in a rural region in northern Tunisia were collected. Samples were screened to recover ESBL-Ec, and collected isolates were characterized for phenotype/genotype of antimicrobial resistance, integrons, and molecular typing (pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)). Overall, 47 ESBL-Ec were identified, with the following genes detected: 35 bla_CTX-M-1, 5 bla_CTX-M-55, 5 bla_CTX-M-15, 1 bla_SHV-2, and 1 bla_SHV-12. Resistance to fluoroquinolones, tetracycline, sulfonamides, and colistin was encoded by aac(6')-Ib-cr (n = 21), qnrB (n = 1), and qnrS (n = 2); tetA (n = 17)/tetB (n = 26); sul1 (n = 29)/sul2 (n = 18); and mcr-2 (n = 2) genes, respectively. PFGE and MLST identified genetic homogeneity of isolates in House 1; however, isolates from House 2 were heterogeneous. Notably, among nine identified sequence types, ST58, ST69, ST224, and ST410 belong to pandemic high-risk clonal lineages associated with extrapathogenic E. coli. Minor clones belonging to ST410 and ST471 were shared by chickens from both households. The virulence genes fyuA, fimH, papGIII, and iutA were detected in 35, 47, 17, and 23 isolates, respectively. Findings indicate a high occurrence of ESBL-Ec in free-range chickens and highlight the occurrence of pandemic zoonotic clones.

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.

A systematic review of the current status of carbapenem resistance in Nigeria: Its public health implication for national intervention

Carbapenem antibiotics are considered one of the most effective and the last-resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, with the advent of carbapenem resistance, it becomes obvious that quality health-care delivery will be hampered if adequate measure is not put in place. This review assessed the prevalence of carbapenem-resistant Gram-negative bacteria (CR-GNB) and also provided an up-to-date position on carbapenem resistance (CR) in Nigeria. Three electronic databases (Google Scholar, PubMed and African Journal online) were searched for relevant literatures, and 38 articles published between January 2013 and June 2022 that met the criteria for inclusion were recruited into the study. The mean prevalence of CR in Nigeria stands at 21.3%, with the southern and northern regions documenting a mean prevalence of 22.0% and 20.9%, respectively. Most of the reviewed articles were from clinical settings (81.6%), with urine samples (38.7%) constituting the most prevalent clinical sample in which CR-GNB were detected. The preponderance of phenotypic methods (55.3%) over molecular method (44.7%), particularly the use of disk diffusion test breakpoint and Modified Hodge test was documented. The most prevalent carbapenem-resistant bacteria were Escherichia coli (50.0%) and Klebsiella pneumoniae (26.3%). The blaNDM and blaVIM were the major reported carbapenemase-encoded genes, particularly among E. coli, K. pneumoniae and Pseudomonas species. This systematic review revealed a mean prevalence of CR-GNB in Nigeria that required urgent attention. Furthermore, the detection of clinically and epidemiologically important carbapenemase coding genes is of public health importance.

Plasmid Carrying blaCTX-M-15, blaPER-1, and blaTEM-1 Genes in Citrobacter spp. From Regional Hospital in Mexico

Introduction:

Citrobacter spp. is an opportunistic bacteria that have been recognized as significant pathogens in patients with underlying diseases or immunocompromised status. The aim of this study was to identify extended-spectrum β-lactamases in clinical isolates of Citrobacter spp.

Methods:

This cross-sectional study was conducted at Hospital Central “Dr. Ignacio Morones Prieto” in San Luis Potosi, Mexico. Nineteen isolates of Citrobacter spp. were obtained from clinical specimens between April to December 2015. Four isolates were resistant to third-generation cephalosporins. The presence of genes encoding ESBL ( blaCTX-M-15, blaTEM-1, blaVEB-1, blaSHV, and blaPER-1) was analyzed by PCR. For this purpose, plasmid DNA was extracted and horizontally transferred to recipient E. coli Top 10.

Results:

blaCTX-M-15 and blaVEB-1 genes were detected in Citrobacter freundii and Citrobacter sedlakii, whereas blaPER-1 gene was identified in 1 isolate of Citrobacter freundii. In contrast, blaSHV gene was not detected in any isolate. One strain carried blaCTX-M-15, blaTEM-1, blaVEB-1, and blaPER-1 genes, most in a 275-kb plasmid.

Conclusion:

This study shows the presence of different types of ESBL in clinical isolates of Citrobacter freundii and Citrobacter sedlakii, which confer resistance to broad-spectrum β-lactams. The plasmid identified in this study harboring ESBL genes could play an important role in the dissemination of antibiotic resistance.

Genetic characterization of ESBL/pAmpC-producing Escherichia coli isolated from forest, urban park and cereal culture soils

Little is known about the role of forestland and non-fertilized agriculture soils as reservoirs of extended-spectrum beta-lactamase (ESBL) and plasmid-borne AmpC (pAmpC)-producing Escherichia coli isolates. Thus, in the present study, 210 soil samples from various origins (forest of Oued Zen (Ain Drahem), non-agriculture soils from different park gardens in Tunis City, cereal culture soils and home gardens) were investigated to characterize cefotaxime-resistant E. coli isolates. A total of 22 ESBL/pAmpC-producing E. coli were collected, and all harbored variants of the blaCTX-M gene (15 blaCTX-M-1, 5 blaCTX-M-55 and 2 blaCTX-M-15). A total of seven and two isolates harbored also blaEBC and blaDHA-like genes, respectively. Resistances to tetracycline, sulfonamides and fluoroquinolones were encoded by tetA (n = 4)/tetB (n = 12), sul1 (n = 17)/sul2 (n = 19) and aac(6')-Ib-cr (n = 2)/qnrA (n = 1)/qnrS (n = 1) genes, respectively. A total of seven isolates were able to transfer by conjugation cefotaxime-resistance in association or not with other resistance markers. PFGE showed that ten and two isolates were clonally related (pulsotypes P1 and P2). The 10 P1 isolates had been collected from forestland, cereal culture soils and an urban park garden in Tunis City, arguing for a large spread of clonal strains. Our findings highlight the occurrence of ESBL/pAmpC-E. coli isolates in soils under limited anthropogenic activities and the predominance of CTX-M enzymes that are largely disseminated in E. coli from humans and animals in Tunisia.

Genetic Environments of Plasmid-Mediated blaCTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.

Prevalence of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Ethiopia: A Systematic Review and Meta-Analysis

Background

Antimicrobial resistance especially caused by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has become a global public health concern. Globally, these isolates have remained the most important causes of several infections and associated mortality. Their rapid spread in Ethiopia is associated with a lack of regular surveillance and antibiotic stewardship programs. Isolates of ESBL-PE from different regions of Ethiopia were searched exhaustively. However, published data regarding the pooled estimate of ESBL-PE are not conducted in Ethiopia. For this reason, we systematically reviewed laboratory-based studies to summarize the overall pooled prevalence of the isolates recovered from various human specimens.

Methods

An exhaustive literature search was carried out using the major electronic databases including PubMed, Web of Science, MEDLINE, EMBASE, CINAHL, Google Scholar, Cochrane Library, Scopus, and Wiley Online Library to identify potentially relevant studies without date restriction. Original articles which address the research question were identified, screened, and included using the PRISMA follow diagram. Data extraction form was prepared in Microsoft Excel, and data quality was assessed by using 9-point Joanna Briggs Institute critical appraisal tools. Then, data were exported to STATA 16.0 software for analyses of pooled estimation of outcome measures. Estimation of outcome measures at 95% confidence interval was performed using Der-Simonian-Laird's random-effects model. Finally, results were presented via text, figures, and tables.

Results

A comprehensive electronic database literature search has yielded a total of 86 articles. Among the total, 68 original articles were excluded after the review process. A total of 18 studies with 1191 bacterial isolates recovered from 7919 various clinical samples sizes were included for systematic review and meta-analysis. In this study, the pooled prevalence of ESBL-PE was 18% (95% CI: 9–26). Nine out of the total (50%) reviewed articles were studied using the combination disk test. Likewise, E. coli and K. pneumoniae (50% both) were the predominant isolates of ESBL-PE in addition to other isolates such as Salmonella spp. and Shigella spp.

Conclusion

This meta-analysis has shown a low pooled estimate of ESBL-PE in Ethiopia.

Antimicrobial resistance: more than 70 years of war between humans and bacteria

Development of antibiotic resistance in bacteria is one of the major issues in the present world and one of the greatest threats faced by mankind. Resistance is spread through both vertical gene transfer (parent to offspring) as well as by horizontal gene transfer like transformation, transduction and conjugation. The main mechanisms of resistance are limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. The highest quantities of antibiotic concentrations are usually found in areas with strong anthropogenic pressures, for example medical source (e.g., hospitals) effluents, pharmaceutical industries, wastewater influents, soils treated with manure, animal husbandry and aquaculture (where antibiotics are generally used as in-feed preparations). Hence, the strong selective pressure applied by antimicrobial use has forced microorganisms to evolve for survival. The guts of animals and humans, wastewater treatment plants, hospital and community effluents, animal husbandry and aquaculture runoffs have been designated as "hotspots for AMR genes" because the high density of bacteria, phages, and plasmids in these settings allows significant genetic exchange and recombination. Evidence from the literature suggests that the knowledge of antibiotic resistance in the population is still scarce. Tackling antimicrobial resistance requires a wide range of strategies, for example, more research in antibiotic production, the need of educating patients and the general public, as well as developing alternatives to antibiotics (briefly discussed in the conclusions of this article).

An African perspective on the prevalence, fate and effects of carbapenem resistance genes in hospital effluents and wastewater treatment plant (WWTP) final effluents: A critical review

This article provides an overview of the antibiotic era and discovery of earliest antibiotics until the present day state of affairs, coupled with the emergence of carbapenem-resistant bacteria. The ways of response to challenges of antibiotic resistance (AR) such as the development of novel strategies in the search of new antibiotics, designing more effective preventive measures as well as the ecology of AR have been discussed. The applications of plant extract and chemical compounds like nanomaterials which are based on recent developments in the field of antimicrobials, antimicrobial resistance (AMR), and chemotherapy were briefly discussed. The agencies responsible for environmental protection have a role to play in dealing with the climate crisis which poses an existential threat to the planet, and contributes to ecological support towards pathogenic microorganisms. The environment serves as a reservoir and also a vehicle for transmission of antimicrobial resistance genes hence, as dominant inhabitants we have to gain a competitive advantage in the battle against AMR.

Sharing of Clinically Important Antimicrobial Resistance Genes by Companion Animals and Their Human Household Members

The aims of this study were to implement a rapid easy methodology, to characterize the antimicrobial resistance gene (AMR) gut content associated with Enterobacteriales and staphylococci; and to evaluate statistical association between AMRs present in fecal samples from healthy companion animals and their human household members. Fecal samples were collected from 27 humans and 29 companion animals living in close contact in 20 households. Nineteen healthy humans without daily contact with companion animals were the control group. After DNA extraction, β-lactamase families and 10 genes of other antimicrobial classes were screened by PCR. Furthermore, third-generation cephalosporin-resistant, carbapenem-resistant, and colistin-resistant Enterobacteriales and methicillin-resistant staphylococci were screened by bacteriological methods. The bla_TEM-1B gene with a P3 promotor was the most frequent β-lactam-resistant gene detected in humans and companion animals from households (33.3%, and 17.2%, respectively). The sul2 was the most frequently shared gene by humans and animals from the same household. In 50% of households at least one AMR was detected simultaneously in companion animal/owner pairs. Healthy humans and companion animals carried several AMRs of clinical importance. To the best our knowledge, this study reports the first detection of the bla_SHV-27 gene in fecal samples from healthy humans in Portugal and in Europe.

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world

Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.

Look and Outlook on Enzyme-Mediated Macrolide Resistance

Since their discovery in the early 1950s, macrolide antibiotics have been used in both agriculture and medicine. Specifically, macrolides such as erythromycin and azithromycin have found use as substitutes for β-lactam antibiotics in patients with penicillin allergies. Given the extensive use of this class of antibiotics it is no surprise that resistance has spread among pathogenic bacteria. In these bacteria different mechanisms of resistance have been observed. Frequently observed are alterations in the target of macrolides, i.e., the ribosome, as well as upregulation of efflux pumps. However, drug modification is also increasingly observed. Two classes of enzymes have been implicated in macrolide detoxification: macrolide phosphotransferases and macrolide esterases. In this review, we present a comprehensive overview on what is known about macrolide resistance with an emphasis on the macrolide phosphotransferase and esterase enzymes. Furthermore, we explore how this information can assist in addressing resistance to macrolide antibiotics.

Dissemination and genetic support of broad-spectrum beta-lactam-resistant Escherichia coli strain isolated from two Tunisian hospitals during 2004-2012

BACKGROUND

The dissemination of extended-spectrum β-lactamase (ESBL)-producing bacteria presented a great concern worldwide. Gram-negative organisms such as Escherichia coli and Klebsiella pneumoniae are the most frequently isolated pathogens responsible for nosocomial infections.

OBJECTIVES

The aim of this study was to investigate and to follow the emergence of resistance and the characterization of Extended-Spectrum Beta-Lactamases (ESBL) among broad-spectrum beta-lactam-Escherichia coli clinical isolates recovered from the military hospital and Habib Thameur hospital in Tunisia.

METHODS

A total of 113 E.coli isolates obtained during the period 2004 through 2012 showed a significant degree of multi-resistance. Among these strains, the double-disk synergy test confirmed the ESBL phenotype in 46 isolates. These included 32(70%) strains from Hospital A and 14(30%) from Hospital B.

RESULTS

The ESBL was identified as CTX-M-15. The ESBL resistance was transferred by a 60 kb plasmid CTXM-15-producing isolates were unrelated according to the PFGE analysis and characterization of the regions surrounding the blaCTX-M-15 showed the ISEcp1 elements located in the upstream region of the bla gene and 20 of them truncated by IS26.

CONCLUSION

ESBL producing E. coli strains are a serious threat in the community in Tunisia and we should take into consideration any possible spread of such epidemiological resistance.

The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments

Class 1 integrase intI1 has been considered as a good proxy for anthropogenic pollution because of being linked to genes conferring resistance to antibiotics. The gene cassettes of class 1 integrons could carry diverse antibiotic resistance genes (ARGs) and conduct horizontal gene transfer among microorganisms. The present study applied high-throughput sequencing technique combined with an intI1 database and genome assembly to quantify the abundance of intI1 in 64 environmental samples from 8 ecosystems, and to investigate the diverse arrangements of ARG-carrying gene cassettes (ACGCs) carried by class 1 integrons. The abundance of detected intI1 ranged from 3.83 × 10^-4 to 4.26 × 10° intI1/cell. High correlation (Pearson's r = 0.852) between intI1 and ARG abundance indicated that intI1 could be considered as an important indicator of ARGs in environments. Aminoglycoside resistance genes were most frequently observed on gene cassettes, carried by 57% assembled ACGCs, followed by trimethoprim and beta-lactam resistance genes. This study established the pipeline for broad monitoring of intI1 in various environmental samples and scanning the ARGs carried by integrons. These findings supplemented our knowledge on the distribution of class 1 integrons and ARGs carried on mobile genetic elements, benefiting future studies on horizontal gene transfer of ARGs.

Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Pharmaceutical Wastewaters in South-Western Nigeria

Emergence and spread of Klebsiella pneumoniae isolates producing extended-spectrum β-lactamases (ESBLs) present a major threat to public health. In this study, we characterized β-lactam-resistant K. pneumoniae isolates from six wastewater samples obtained from two pharmaceutical industries located in Lagos and Ogun States, Nigeria. Bacteria were isolated by using MacConkey agar; species identification and antibacterial susceptibility testing were performed by Vitek 2. Etest was used for ESBL phenotype confirmation. The presence of β-lactamase genes was investigated by PCR and sequencing. Bacterial strain typing was done by XbaI-macrorestriction and subsequent pulsed-field gel electrophoresis (PFGE) as well as multilocus sequence typing (MLST). Thirty-five bacterial species were isolated from the six samples; among them, we identified seven K. pneumoniae isolates with resistance to β-lactams and co-resistance to fluoroquinolones, aminoglycosides, and folate pathway inhibitors. The ESBL phenotype was confirmed in six K. pneumoniae isolates that harbored ESBL genes bla_CTX-M-15 (n = 5), bla_SHV-2 (n = 1), and bla_SHV-12 (n = 1). PFGE and MLST analysis revealed five clones belonging to four sequence types (ST11, ST15, ST37, ST101), and clone K. pneumoniae-ST101 was present in the wastewater samples from two different pharmaceutical industries. Additionally performed conjugation assays confirmed the location of β-lactamase genes on conjugative plasmids. This is the first confirmation of K. pneumoniae isolates producing CTX-M-15-ESBL from pharmaceutical wastewaters in Nigeria. The co-resistance observed might be a reflection of the different drugs produced by these industries. Continuous surveillance of the environmental reservoirs of multidrug-resistant bacteria is necessary to prevent their further spread.

Genotyping and characterization of CTX-M-15 -producing Klebsiella pneumoniae isolated from an Iranian hospital

The aims were to describe the genetic characterization of blaCTX-M-1 group gene in Klebsiella pneumoniae and to investigate the relationship between isolates by MLVA and PFGE. We analyzed 36 CTX-M group 1-ESBL producing K. pneumoniae. rmpA and wcaG virulence genes were identified by PCR. The genetic environment of blaCTX-M-1 was analyzed by PCR and sequencing. Plasmid replicons were determined using PCR-based replicon typing. The isolates were typed by MLVA and PFGE. All blaCTX-M-1 were blaCTX-M-15. The wcaG and rmpA were detected in 1 and 2 isolates, respectively. IncF were the most frequently detected replicons (63.88%). In all isolates, ISEcp1 was found upstream and orf477 downstream of blaCTX-M-15, IS26 was found in two isolates. MLVA identified 20 MLVA types, whereas PFGE identified 25 different profiles. The dissemination of CTX-M-15 in our isolates was due to the clonal spread of isolates and to the genetic transfer of mobile elements among unrelated strains.

Distribution of virulence genes and genotyping of CTX-M-15-producing Klebsiella pneumoniae isolated from patients with community-acquired urinary tract infection (CA-UTI)

Klebsiella pneumoniae is one of the most important agents of community-acquired urinary tract infection (CA-UTI). In addition to extended-spectrum β-lactamases (ESBLs), a number of virulence factors have been shown to play an important role in the pathogenesis of K. pneumoniae, including capsule, siderophores, and adhesins. Little is known about the genetic diversity and virulence content of the CTX-M-15-producing K. pneumoniae isolated from CA-UTI in Iran. A total of 152 K. pneumoniae isolates were collected from CA-UTI patients in Tehran from September 2015 through April 2016. Out of 152 isolates, 40 (26.3%) carried bla_CTX-M-15. PCR was performed for detection of virulence genes in CTX-M-15-producing isolates. Furthermore, all of these isolates were subjected to multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA). Using MLVA method, 36 types were identified. CTX-M-15-producing K. pneumoniae isolates were grouped into 5 clonal complexes (CCs). Of these isolates, mrkD was the most prevalent virulence gene (95%), followed by kpn (60%), rmpA (37.5%), irp (35%), and magA (2.5%). No correlation between MLVA types or CCs and virulence genes or antibiotic resistance patterns was observed. Overall, it is thought that CTX-M-15-producing K. pneumoniae strains isolated from CA-UTI have arisen from different clones.

Resistance to Macrolide Antibiotics in Public Health Pathogens

Macrolide resistance mechanisms can be target-based with a change in a 23S ribosomal RNA (rRNA) residue or a mutation in ribosomal protein L4 or L22 affecting the ribosome's interaction with the antibiotic. Alternatively, mono- or dimethylation of A2058 in domain V of the 23S rRNA by an acquired rRNA methyltransferase, the product of an erm (erythromycin ribosome methylation) gene, can interfere with antibiotic binding. Acquired genes encoding efflux pumps, most predominantly mef(A) + msr(D) in pneumococci/streptococci and msr(A/B) in staphylococci, also mediate resistance. Drug-inactivating mechanisms include phosphorylation of the 2'-hydroxyl of the amino sugar found at position C5 by phosphotransferases and hydrolysis of the macrocyclic lactone by esterases. These acquired genes are regulated by either translation or transcription attenuation, largely because cells are less fit when these genes, especially the rRNA methyltransferases, are highly induced or constitutively expressed. The induction of gene expression is cleverly tied to the mechanism of action of macrolides, relying on antibiotic-bound ribosomes stalled at specific sequences of nascent polypeptides to promote transcription or translation of downstream sequences.

A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous

β-lactamases are the primary cause of resistance to β-lactams among members of the family Enterobacteriaceae. SHV enzymes have emerged in Enterobacteriaceae causing infections in health care in the last decades of the Twentieth century, and they are now observed in isolates in different epidemiological settings both in human, animal and the environment. Likely originated from a chromosomal penicillinase of Klebsiella pneumoniae, SHV β-lactamases currently encompass a large number of allelic variants including extended-spectrum β-lactamases (ESBL), non-ESBL and several not classified variants. SHV enzymes have evolved from a narrow- to an extended-spectrum of hydrolyzing activity, including monobactams and carbapenems, as a result of amino acid changes that altered the configuration around the active site of the β -lactamases. SHV-ESBLs are usually encoded by self-transmissible plasmids that frequently carry resistance genes to other drug classes and have become widespread throughout the world in several Enterobacteriaceae, emphasizing their clinical significance.

Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from blood cultures in Africa

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae have been isolated from many regions of the world. Epidemiological studies are being conducted in Europe, North America, and Asia. No study has however been conducted in Africa to determine the prevalence and distribution of ESBLs on the continent. This literature review aimed at describing the prevalence of ESBL-producing Enterobacteriaceae isolated from blood cultures, as well as the ESBL genes involved at the international level. Our focus was mainly on Africa. We conducted a literature review on PubMed. Articles related to our study field and published between 1996 and 2014 were reviewed and entirely read for most of them, while we only focused on the abstracts of some other articles. Relevant articles to our study were then carefully reviewed and included in the review. The prevalence of ESBL-producing Enterobacteriaceae differs from one country to another. The results of our literature review however indicate that class A ESBLs prevail over the other types. We took into consideration articles focusing on various types of samples to assess the prevalence of ESBL-producing Enterobacteriaceae, but information on isolates from blood cultures is limited. The worldwide prevalence of ESBL-producing Enterobacteriaceae has increased over time. Evidence of ESBL-producing Enterobacteriaceae can be found in all regions of the world. Studies conducted in Africa mainly focused on the Northern and Eastern parts of the continent, while only rare studies were carried out in the rest of the continent.

ESBL-producing Enterobacteriaceae in Africa - a non-systematic literature review of research published 2008-2012

INTRODUCTION

Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBL) has been found all over the world, and risk factors for acquiring these bacteria involve hospital care and antibiotic treatment. Surveillance studies are present in Europe, North America, and Asia, but there is no summarizing research published on the situation in Africa.

AIM

This review aims to describe the prevalence of ESBL-producing Enterobacteriaceae in hospital and community settings in Africa and the ESBL genes involved.

METHOD

A non-systematic literature search was performed in PubMed. All articles published between 2008 and 2012 were screened and read in full text. Relevant articles were assessed for quality of evidence and included in the review. Articles were divided into regional areas in Africa and tabulated.

RESULTS

ESBL-producing Enterobacteriaceae in hospitalized patients and in communities varies largely between countries and specimens but is common in Africa. ESBLs (class A and D) and plasmid-encoded AmpC (pAmpC) were regularly found, but carbapenemases were also present.

CONCLUSION

ESBL-producing Enterobacteriaceae in hospital and community settings in Africa is common. Surveillance of antimicrobial resistance needs to be implemented in Africa to tailor interventions targeted at stopping the dissemination of ESBL-producing Enterobacteriaceae.

blaCTX-M-15-carrying F2:A-:B- plasmid in Escherichia coli from cattle milk in Tunisia

Extended-spectrum β-lactamases (ESBL) are widespread enzymes in animals, and the risk of transmission of ESBL genes to humans has become a major issue. In Tunisia, recent data showed a high prevalence of ESBL-producing Escherichia coli isolates in healthy animals, mostly in chickens. In this study, we report the first data on ESBL in diseased Tunisian animals (chickens and cattle), highlighting a major difference in ESBL prevalence in the infectious versus noninfectious E. coli flora. Interestingly, the only ESBL producer was an ST10 E. coli from a cattle, and not from chicken. Moreover, this E. coli isolate harbored the bla(CTX-M-15) gene on an F2:A-:B- plasmid, a combination frequently found in humans. This plasmid was also highly similar to a bla(CTX-M-15) F2:A-:B- plasmid recently reported in cattle in France. Altogether, this study is also the first report of the bla(CTX-M-15) gene in food animals in Tunisia, and, to our best knowledge, the first report of an ESBL producer in cattle in Africa. Since this plasmid was recognized in cattle in France and worldwide in humans, the question of its origin in Tunisian cattle is open. The detection of ESBL producers in milk in Tunisia may also constitute a risk of ESBL transmission from animals to humans through food consumption.

Occurrence of clinical isolates ofKlebsiella pneumoniaeharboring chromosomally mediated and plasmid-mediated CTX-M-15 β-lactamase in a Tunisian hospital

The spread of multidrug-resistant strains of Klebsiella pneumoniae in hospitals is of concern to clinical microbiologists, health care professionals, and physicians because of the impact infections caused by these bacteria have in causing morbidity and mortality. Clinical isolates of K. pneumoniae have been found to show resistance to third-generation cephalosporins as a result of acquiring extended-spectrum β-lactamase-producing genes, such as blaCTX-M. Since little is known about the mechanisms of antibiotic resistance observed in Kasserine hospital, Tunisia, this study was undertaken to investigate the mechanisms by which clinical isolates of K. pneumoniae resist β-lactam antibiotics. Twelve strains of K. pneumoniae were collected from patients admitted to Kasserine hospital; these isolates showed multiresistance phenotypes. Molecular genetics investigations using polymerase chain reaction, S1 digestion, and pulsed-field gel electrophoresisshowed that blaCTX-M-15in association with ISEcp1 is responsible for the resistance of these strains to third-generation cephalosporins. It has been determined that blaCTX-M-15is chromosomally mediated and plasmid mediated, which alarming need for infection control to prevent the outbreak of such a resistance mechanism.

Loss of hairless confers susceptibility to UVB-induced tumorigenesis via disruption of NF-kappaB signaling

In order to model squamous cell carcinoma development in vivo, researchers have long preferred hairless mouse models such as SKH-1 mice that have traditionally been classified as ‘wild-type’ mice irrespective of the genetic factors underlying their hairless phenotype. The work presented here shows that mutations in the Hairless (Hr) gene not only result in the hairless phenotype of the SKH-1 and Hr^−/− mouse lines but also cause aberrant activation of NFκB and its downstream effectors. We show that in the epidermis, Hr is an early UVB response gene that regulates NFκB activation and thereby controls cellular responses to irradiation. Therefore, when Hr expression is decreased in Hr mutant animals there is a corresponding increase in NFκB activity that is augmented by UVB irradiation. This constitutive activation of NFκB in the Hr mutant epidermis leads to the stimulation a large variety of downstream effectors including the cell cycle regulators cyclin D1 and cyclin E, the anti-apoptosis protein Bcl-2, and the pro-inflammatory protein Cox-2. Therefore, Hr loss results in a state of uncontrolled epidermal proliferation that promotes tumor development, and Hr mutant mice should no longer be considered merely hairless 'wild-type' mice. Instead, Hr is a crucial UVB response gene and its loss creates a permissive environment that potentiates increased tumorigenesis.

Characterization and molecular epidemiology of extended spectrum beta-lactamase producing Enterobacter cloacae isolated from a Tunisian hospital

In 2009, out of the 66 nonrepetitive Enterobacter cloacae collected at Charles Nicolle hospital in Tunisia, 44 were extended spectrum β-lactamase (ESBL) producers. The aim of the current study was to detect and characterize the genes encoding the ESBLs including blaTEM, blaSHV, and blaCTX-M groups by polymerase chain reaction and sequencing. Pulsed-field gel electrophoresis (PFGE) analysis was used to determine the genetic relatedness between isolates. All strains were susceptible to carbapenems. They were resistant to fluoroquinolones, gentamicin, tobramycin, and trimethoprim+sulfamethoxazole but variably resistant to netilmicin, amikacin, and tetracyclines. Sequence analysis of the polymerase chain reaction products revealed the presence of blaCTX-M-15 (39 strains), blaSHV-12 (6 strains), and blaSHV-27 (1 strain). The coexistence of two ESBLs was observed in two isolates harboring, respectively, SHV-12+CTX-M-15 and SHV-27+CTX-M-15. PFGE revealed 36 unrelated profiles. Diffusion of E. cloacae producing CTX-M-15 ESBL in our hospital is the consequence of dissemination of identical or related plasmids harboring the CTX-M-15 gene.

Evolution of β-lactams resistance in Gram-negative bacteria in Tunisia

Antimicrobial resistance is a major health problem worldwide, but marked variations in the resistance profiles of bacterial pathogens are found between countries and in different patient settings. In Tunisia, the strikingly high prevalence of resistance of bacteria to penicillins and cephalorosporins drugs including fourth generation in clinical isolates of Gram negative bacteria has been reported. During 30 years, the emerging problem of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates is substantial, and some unique enzymes have been found. Recently, evidence that Gram-negative bacteria are resistant to nearly all available antimicrobial agents, including carbapenems, have emerged.

Serotypes, antibiotic resistance, and class 1 integrons in Salmonella isolates from pediatric cases of enteritis in Tehran, Iran

The present study was conducted to investigate serotype distribution, antimicrobial resistance patterns, carriage of class 1 integron, and clonality of Salmonella strains isolated from patients aged 0-12 years in Tehran, Iran, during 2007-2008. A total of 139 Salmonella isolates were studied. Salmonella serotypes Enteritidis, Infantis, and Typhimurium included 84.9% of isolates, Enteritidis accounting for 41.7%. The most prevalent resistances were to doxycycline (64.7%), nalidixic acid (61.2%), tetracycline (51.8%), and streptomycin (42.8%). Fifty-three (38.1%) isolates contained class 1 integron. Eight different gene cassettes were identified, aadA1 being the most frequently encountered. Pulsed-field gel electrophoresis showed that integron-positive Salmonella strains belonging to serotypes Infantis, Enteritidis, and Typhimurium were attributed to two, three, and five different pulsotypes, respectively. The findings indicated that the distribution and drug resistance pattern of most prevalent Salmonella serotypes were broadly similar to that reported globally from human isolates. Presence of class 1 integrons was common among Salmonella serotypes in Tehran, Iran. Concurrent clonal expansion and horizontal transmission events seem to contribute to increase in drug resistance prevalence among Salmonella serotypes.

SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

Background

SHV β-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (http://www.lahey.org/Studies/). Besides, information about SHV β-lactamases can be found in the rapidly growing NCBI protein database. The SHV β-Lactamase Engineering Database (SHVED) has been developed to collect the SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions.

Description

The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.

The SHVED is accessible at http://www.LacED.uni-stuttgart.de/classA/SHVED/. It provides sequences, structures, and a multisequence alignment of SHV β-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download.

Conclusions

The SHV β-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV β-lactamases.

High prevalence of bla(CTX-M) extended spectrum beta-lactamase genes in Klebsiella pneumoniae isolates from a tertiary care hospital: first report of bla(SHV-12), bla(SHV-31), bla(SHV-38), and bla(CTX-M-15) in Brazil

The aim of this study was to investigate the presence and prevalence of bla(TEM), bla(SHV), and bla(CTX-M) and bla(GES)-like genes, responsible for extended spectrum beta-lactamases (ESBLs) production in clinical isolates of Klebsiella pneumoniae collected from a Brazilian tertiary care hospital. Sixty-five ESBL producing K. pneumoniae isolates, collected between 2005 and 2007, were screened by polymerase chain reaction (PCR). Identification of bla genes was achieved by sequencing. Genotyping of ESBL producing K. pneumoniae was performed by the enterobacterial repetitive intergenic consensus-PCR with cluster analysis by the Dice coefficient. The presence of genes encoding ESBLs was confirmed in 59/65 (90.8%) isolates, comprising 20 bla(CTX-M-2), 14 bla(CTX-M-59), 12 bla(CTX-M-15), 9 bla(SHV-12), 1 bla(SHV-2), 1 bla(SHV-2a), 1 bla(SHV-5), and 1 bla(SHV-31) genes. The ESBL genes bla(SHV-12), bla(SHV-31), and bla(CTX-M-15), and the chromosome-encoded SHV-type beta-lactamase capable of hydrolyzing imipenem were detected in Brazil for the first time. The analysis of the enterobacterial repetitive intergenic consensus-PCR band patterns revealed a high rate of multiclonal bla(CTX-M) carrying K. pneumoniae isolates (70.8%), suggesting that dissemination of encoding plasmids is likely to be the major cause of the high prevalence of these genes among the K. pneumoniae isolates considered in this study.

Predominance of an ST11 extended-spectrum β-lactamase-producing Klebsiella pneumoniae clone causing bacteraemia and urinary tract infections in Korea

To investigate the antimicrobial resistance, extended-spectrum β-lactamases (ESBLs) and clones of Klebsiella pneumoniae isolates causing bacteraemia or urinary tract infection (UTI) in Korea, a total of 406 K. pneumoniae isolates from patients with bacteraemia (221 isolates) and UTI (185 isolates) were collected from 10 tertiary-care Korean hospitals from July 2006 to October 2007. In vitro antimicrobial susceptibility testing was performed for all isolates and ESBL production was tested. Multilocus sequence typing (MLST) analyses were performed to characterize genotypes of ESBL-producing K. pneumoniae isolates. PFGE was performed for sequence type 11 (ST11) isolates. Forty-seven UTI isolates (25.4 %) produced ESBLs, while 30 bacteraemia isolates (13.6 %) produced ESBLs (P=0.002). Among 77 ESBL-producing isolates, thirty-two (41.6 %) produced SHV-type ESBLs. bla CTX-M genes such as bla CTX-M-14 and bla CTX-M-15 were detected in 36.4 %. MLST and PFGE analyses showed that ST11 was dominant in ESBL-producing K. pneumoniae isolates causing UTI (57.4 %) and in those causing bacteraemia (70.0 %) and has been prevalent in Korean hospitals. ST11 isolates harbour a combination of different ESBL genes. The ST11 clone of ESBL-producing K. pneumoniae isolates prevails in Korea, but most isolates might acquire ESBL genes independently or several different clones might be distributed in Korea.

Prevalence of broad-spectrum cephalosporin-resistant Escherichia coli isolates in food samples in Tunisia, and characterization of integrons and antimicrobial resistance mechanisms implicated

The presence of broad-spectrum-cephalosporin-resistant Escherichia coli isolates and the implicated mechanisms of resistance were investigated in 79 food samples of animal origin obtained in different supermarkets and local butcheries in Tunisia. Ten of these samples (12.6%) harbored extended-spectrum beta-lactamase (ESBL) producing E. coli isolates and 13 ESBL-positive isolates were recovered (one or two/sample), which exhibited nine different Pulsed-Field-Gel-Electrophoresis (PFGE) patterns. ESBLs detected were the following: CTX-M-1 (10 strains), CTX-M-1+TEM-1b (2 strains) and CTX-M-1+TEM-20 (1 strain). The orf477 sequence was identified downstream of bla(CTX-M-1) gene in all 13 strains and ISEcp1 upstream in 9 strains. All ESBL-positive strains were included into phylogenetic group A or B1 (4 and 9 strains, respectively). Three of the 79 food samples (3.8%) contained broad-spectrum-cephalosporin-resistant and ESBL-negative E. coli isolates with AmpC phenotype. One isolate per sample was studied, and they showed unrelated PFGE patterns. The CMY-2 type beta-lactamase was identified in one of these 3 strains and specific point mutations in the promoter/attenuator region of ampC gene (at positions -42, -18, -1 and +58) were detected in the remaining two strains. Twelve ESBL-positive and one ESBL-negative E. coli strains contained class 1 integrons with the following gene cassette arrangements: dfrA1+aadA (6 strains) and dfrA17+aadA5 (7 strains). E. coli strains from food samples could represent a reservoir of ESBL-encoding genes and integrons that could be transmitted to humans through the food chain.