More extended-spectrum beta-lactamases

Discovery of novel dihydronaphthalene-imidazole ligands as potential inhibitors of Staphylococcus aureus multidrug resistant NorA efflux pump: A combination of experimental and in silico molecular docking studies

Overexpression of the efflux pump is a predominant mechanism by which bacteria show antimicrobial resistance (AMR) and leads to the global emergence of multidrug resistance (MDR). In this work, the inhibitory potential of library of dihydronapthyl scaffold-based imidazole derivatives having structural resemblances with some known efflux pump inhibitors (EPI) were designed, synthesized and evaluated against efflux pump inhibitor against overexpressing bacterial strains to study the synergistic effect of compounds and antibiotics. Out of 15 compounds, four compounds (Dz-1, Dz-3, Dz-7, and Dz-8) were found to be highly active. DZ-3 modulated the MIC of ciprofloxacin, erythromycin, and tetracycline by 128-fold each against 1199B, XU212 and RN4220 strains of S. aureus respectively. DZ-3 also potentiated tetracycline by 64-fold in E. coli AG100 strain. DZ-7 modulated the MIC of both tetracycline and erythromycin 128-fold each in S. aureus XU212 and S. aureus RN4220 strains. DZ-1 and DZ-8 showed the moderate reduction in MIC of tetracycline in E. coli AG100 only by 16-fold and 8-fold, respectively. DZ-3 was found to be the potential inhibitor of NorA as determined by ethidium bromide efflux inhibition and accumulation studies employing NorA overexpressing strain SA-1199B. DZ-3 displayed EPI activity at non-cytotoxic concentration to human cells and did not possess any antibacterial activity. Furthermore, molecular docking studies of DZ-3 was carried out in order to understand the possible binding sites of DZ-3 with the active site of the protein. These studies indicate that dihydronaphthalene scaffolds could serve as valuable cores for the development of promising EPIs.

Whole-Genome Sequencing of an Escherichia coli ST69 Strain Harboring blaCTX-M-27 on a Hybrid Plasmid

Objective

Escherichia coli is a common Gram-negative human pathogen. The emergence of E. coli with multiple-antibiotic-resistant phenotypes has become a serious health concern. This study reports the whole-genome sequences of third-generation cephalosporin-resistant (3GC-R) and multidrug-resistant (MDR) E. coli EC6868 and explores the acquired antibiotic-resistance genes (ARGs) as well as their genetic contexts.

Methods

E. coli EC6868 was isolated from a vaginal secretion sample of a pregnant patient in China. The antimicrobial susceptibility was assessed, and whole-genome sequencing was conducted. The acquired ARGs, insertion sequence (IS) elements, and integrons within the genome of E. coli EC6868 were identified, and the genetic contexts associated with the ARGs were analyzed systematically.

Results

E. coli EC6868 was determined to belong to ST69 and harbored a 144.9-kb IncF plasmid (pEC6868-1) with three replicons (Col156, IncFIBAP001918, and IncFII). The ESBL gene blaCTX-M-27 was located on the structure "∆ISEcp1-blaCTX-M-27-IS903B", which was widely present in the species of Enterobacteriales. Other ARGs carried by plasmid pEC6868-1 were mainly located on the 18.9-kb IS26-composite transposon (five copies of intact IS26 and one copy of truncated IS26) composing of IS26-mphA-mrx(A)-mphR(A)-IS6100, ∆TnAs3-eamA-tet(A)-tetR(A)-aph(6)-Id-aph(3")-Ib-sul2-IS26, and a class 1 integron, which was widely present on IncF plasmids of E. coli, mainly distributed in ST131, ST38, and ST405. Notably, pEC6868 in our study was the first report on a plasmid harboring the 18.9-kb structure in E. coli ST69 in China.

Conclusion

The 3GC-R E. coli ST69 strain with an MDR IncF plasmid carrying blaCTX-M-27 and other ARGs, conferring resistance to aminoglycosides, macrolides, sulfonamides, tetracycline, and trimethoprim, was identified in a hospital in China. Mobile genetic elements including ISEcp1, IS903B, IS26, Tn3, IS6100 and class 1 integron were found within the MDR region, which could play important roles in the global dissemination of these resistance genes.

A multicentre study to determine the in vitro efficacy of flomoxef against extended-spectrum beta-lactamase producing Escherichia coli in Malaysia

Background

The high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.

Methods

Therefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.

Results

A total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1, blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.

Electroacoustic Biosensor Systems for Evaluating Antibiotic Action on Microbial Cells

Antibiotics are widely used to treat infectious diseases. This leads to the presence of antibiotics and their metabolic products in the ecosystem, especially in aquatic environments. In many countries, the growth of pathogen resistance to antibiotics is considered a threat to national security. Therefore, methods for determining the sensitivity/resistance of bacteria to antimicrobial drugs are important. This review discusses the mechanisms of the formation of antibacterial resistance and the various methods and sensor systems available for analyzing antibiotic effects on bacteria. Particular attention is paid to acoustic biosensors with active immobilized layers and to sensors that analyze antibiotics directly in liquids. It is shown that sensors of the second type allow analysis to be done within a short period, which is important for timely treatment.

Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones

For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success is attributable to the introduction and extensive use in the clinical practice of antibiotics over the course of the last seven decades. In hospital settings, Klebsiella pneumoniae represents a well-known and commonly described opportunistic pathogen, typically characterized by resistance to several antibiotic classes. On the other hand, the broad wedge of population living in Low and/or Middle Income Countries is increasing rapidly, allowing the spread of several commensal bacteria which are transmitted via human contact. Community transmission has been the original milieu of K. pneumoniae isolates characterized by an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged as different pathways in the evolutionary history of K. pneumoniae. For a long time, the Sequence Type (ST), which is defined by the combination of alleles of the 7 housekeeping genes of the Multi-Locus Sequence Typing, has been a reliable marker of the pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) in the Western world and hypervirulent clones (e.g. ST23, ST65, ST86) in the Eastern. Currently, the boundaries separating the two pathotypes are fading away due to several factors, and we are witnessing a worrisome convergence in certain high-risk clones. Here we review the evidence available on confluence of multidrug-resistance and hypervirulence in specific K. pneumoniae clones.

Prevalence of extended spectrum beta lactamase and molecular detection of blaTEM, blaSHV and blaCTX-M genotypes among Gram negative bacilli isolates from pediatric patient population in Gaza strip

BACKGROUND

Extended-spectrum β lactamases (ESBLs), have the ability to hydrolyze and cause resistance to various types of the β-lactam antibiotics, including the extended-spectrum (or third-generation) cephalosporins (e.g., cefotaxime, ceftriaxone, ceftazidime) and monobactams (e.g., aztreonam). ESBL-producing Gram negative bacteria is still posing significant therapeutic challenges.

OBJECTIVES

To assess the prevalence and molecular characteristics of ESBL producing Gram negative bacilli, isolated from a cohort of pediatric patients in Gaza hospitals.

METHODS

A total of 322 isolates of Gram-negative bacilli were collected from four referral pediatric hospitals in Gaza, namely: Al-Nasr, Al-Rantisi, Al-Durra and Beit Hanoun hospitals. These isolates were tested for ESBL production using the double disk synergy and CHROMagar phenotypic methods. Molecular characterization of the ESBL producing strains was performed using PCR targeting the CTX-M, TEM and SHV genes. Antibiotic profile was done using Kirby Bauer method according to Clinical and Laboratory Standard Institute.

RESULTS

Out of 322 isolates tested by phenotypic methods, 166 (51.6%) were ESBL positive. The prevalence of ESBL production in Al-Nasr, Al-Rantisi, Al-Durra and Beit Hanoun hospitals was 54%, 52.5%, 45.5% and 52.8% respectively. The prevalence of ESBL production among Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., Proteus mirabilis, Enterobacter spp., Citrobacter spp., and Serratia marcescens is 55.3%, 63.4%, 17.8%, 57.1%, 33.3%, 28.5%, 38.4%, and 4% respectively. ESBL production among urine, pus, blood, CSF and sputum was 53.3%, 55.2%, 47.4%, 33.3%, and 25% respectively. Out of the 322 isolates, 144 were screened for CTX-M, TEM and SHV production. Using PCR, 85 (59%) had at least one gene. The prevalence rate of CTX-M, TEM and SHV genes was 60%, 57.6%, and 38.3% respectively. Meropenem and amikacin were highest rates of susceptibility antibiotics against ESBLs producers (83.1% and 82.5% respectively), while the least effective antibiotics were amoxicillin (3.1%) and cephalexin (13.9%). Moreover, ESBLs producers showed high resistance rate to cefotaxime, ceftriaxone and ceftazidime (79.5%, 78.9% and 79.5% respectively).

CONCLUSION

Our results show high prevalence of ESBL production among Gram negative bacilli isolated from children in different pediatric hospitals in Gaza strip. A substantial level of resistance to first and second generation cephalosporins was also observed. This ascertains the need for a rational antibiotic prescription and consumption policy.

Characterization of Two Novel AmpC Beta-Lactamases from the Emerging Opportunistic Pathogen, Cedecea neteri

The genus Cedecea (family Enterobacteriaceae) causes a wide spectrum of acute infections in immunocompromised hosts, from pneumonia and bacteremia to oral ulcers and dialysis-related peritonitis. While Cedecea infections are reported infrequently in the literature, documented clinical cases of this emerging opportunistic human pathogen have occurred worldwide. Cedecea neteri has clinical significance and exhibits antimicrobial drug resistance. However, little is known about the molecular basis underlying the resistance phenotypes in C. neteri. We previously hypothesized that the open-reading frame cnt10470 in the C. neteri SSMD04 genome encodes a chromosomal Ambler class C (AmpC) β-lactamase based on sequence homology. In this study, recombinant polyhistidine-tagged proteins were created by cloning the putative ampC genes from SSMD04 and C. neteri ATCC 33855 (a clinical isolate) into the pET-6xHN expression vector, overexpressing the proteins, and then purifying the recombinant AmpCs (rAmpCs) using immobilized metal affinity chromatography (Ni-NTA). The in vitro enzymatic analysis of the purified rAmpCs was performed to determine the K_m and k_cat for various β-lactam substrates. The rAmpCs are functional class C β-lactamases when assayed using the chromogenic β-lactamase substrate, nitrocefin. The presence of functional AmpCs in both C. neteri strains underscores the necessity of performing antibiotic susceptibility testing in the management of C. neteri infections.

Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health

Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.

Insights into nitrogen removal from seawater-based wastewater through marine anammox bacteria under ampicillin stress: Microbial community evolution and genetic response

Global spread of ampicillin (AMP) in the aquatic environment have attracted much attention recently. Marine anammox bacteria (MAB) have potentials in saline wastewater treatment due to their good salt tolerance. However, to date, the effect resulting from AMP on MAB is still unknown. Herein, the effect of AMP on MAB, involving microbial community evolution and genetic response, was investigated for the first time. A lab-scale reactor inoculated by MAB sludge was operated under saline condition (35 g/L) and AMP stress of different gradients. Within 200 cycles, nitrogen removal performance was monitored and sludge samples were withdrawn for high-throughput sequencing analyses and qPCR. The results confirmed that the nitrogen removal capacity of MAB declined with increasing AMP dosage, and almost collapsed at 300 mg/L AMP. The total nitrogen removal rate and specific anammox activity finally dropped to 0.17 kg N m^-3 d^-1 and 101.86 mg N g^-1VSS d^-1, respectively. Pseudoalteromonas (38.13%) dominated the reactor on Cycle 190, which formed a new symbiosis with MAB. And the emergence of oleophilic bacteria such as Colwellia (2.53%) was also observed. Moreover, antibiotic resistance genes were detected with increased abundance and diversity, indicating the AMP dosing significantly promoted microbial community evolution and genetic response.

Revisiting Antibiotic Resistance: Mechanistic Foundations to Evolutionary Outlook

Antibiotics are the pivotal pillar of contemporary healthcare and have contributed towards its advancement over the decades. Antibiotic resistance emerged as a critical warning to public wellbeing because of unsuccessful management efforts. Resistance is a natural adaptive tool that offers selection pressure to bacteria, and hence cannot be stopped entirely but rather be slowed down. Antibiotic resistance mutations mostly diminish bacterial reproductive fitness in an environment without antibiotics; however, a fraction of resistant populations 'accidentally' emerge as the fittest and thrive in a specific environmental condition, thus favouring the origin of a successful resistant clone. Therefore, despite the time-to-time amendment of treatment regimens, antibiotic resistance has evolved relentlessly. According to the World Health Organization (WHO), we are rapidly approaching a 'post-antibiotic' era. The knowledge gap about antibiotic resistance and room for progress is evident and unified combating strategies to mitigate the inadvertent trends of resistance seem to be lacking. Hence, a comprehensive understanding of the genetic and evolutionary foundations of antibiotic resistance will be efficacious to implement policies to force-stop the emergence of resistant bacteria and treat already emerged ones. Prediction of possible evolutionary lineages of resistant bacteria could offer an unswerving impact in precision medicine. In this review, we will discuss the key molecular mechanisms of resistance development in clinical settings and their spontaneous evolution.

Comparative Study of CTX-M-15 Producing Escherichia coli ST131 Clone Isolated from Urinary Tract Infections and Acute Diarrhoea

Background and Purpose

The alarming increase in the prevalence of CTX-M-15 extended-spectrum β-lactamase (ESBL) producing E. coli has been significantly linked to the clonal expansion of emerging sequence type (ST131). This study aimed to screen for the O16/O25-ST131 clones among different phylogenetic types of E. coli strains isolated from urinary and diarrhoeal samples.

Methods

A total of 205 E. coli strains isolated from patients with UTI and acute diarrhoea were investigated by phenotypic and genotypic methods for ESBL identification. Molecular methods were used for identification of O25/O16-ST131 clone and phylogenetic typing of E. coli isolates.

Results

O25-ST131 clone was detected in 89/105 (84.8%) and 47/100 (47%) of urinary and intestinal E. coli isolates, respectively, with a significant difference (P-value<0.001). There was a significant high rate of occurrence of ESBLs, MDR, and antibiotic resistance to most antibiotic classes among O25-ST131 than non-O25-ST131 isolates. CTX-M-15 gene was detected in 64/71 (90%) of ESBLs producing intestinal isolates and 54/79 (68.4%) of urinary ESBLs producing isolates. The O25-ST131 clone was reported among all phylogenetic groups. The O16-ST131 clone serotype was not detected in the study isolates.

Conclusion

High prevalence of the O25-ST131 clone was reported among extraintestinal and intestinal E. coli isolates. First detection of the O25-ST131 clone among phylogenetic groups other than group B2 draws attention of the ability of this clone to transfer among commensal groups. An increasing in the prevalence of CTX-M-15 among E. coli strains especially of intestinal origin is alarming as the intestine is the main reservoir for ExPEC strains causing UTI.

Carriage Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacterales in Outpatients Attending Community Health Centers in Blantyre, Malawi

Antimicrobial resistance due to extended-spectrum β-lactamase (ESBL) production by Enterobacterales is a global health problem contributing to increased morbidity and mortality, particularly in resource-constrained countries. We aimed to determine the prevalence of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) in community patients in Blantyre, Malawi. Clinical samples were collected from 300 patients and screened for ESBL-E using a CHROMagar^TM ESBL medium. Confirmation of ESBL production was done by a combination disk test (CDT). The prevalence of community-acquired ESBL-E was 16.67% (50/300, 95% CI = 12.43–20.91%). The most common ESBL-E species isolated was Escherichia coli (66%). All ESBL-E isolates were resistant to Trimethoprim-Sulfamethoxazole except for 2% of E. coli. Besides this, all ESBL-E were susceptible to Imipenem and only 4% were resistant to Meropenem. No patients with a positive ESBL-E phenotype had a history of hospital admission in the last three months, and the carriage of ESBL-E was neither associated with the demographic nor the clinical characteristics of participants. Our findings reveal a low presence of ESBL-E phenotypes in community patients. The low prevalence of ESBL-E in the community settings of Blantyre can be maintained if strong infection and antimicrobial use-control strategies are implemented.

A novel framework for engineering protein loops exploring length and compositional variation

Insertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with few available platforms capable of systematically generating and analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction digestion and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition-areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.

The magnitude of extended-spectrum beta-lactamase- producing Enterobacteriaceae from clinical samples in Ethiopia: a systematic review and meta-analysis

BACKGROUND

The rapid spread of resistance among extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a serious problem around the world. It results in serious clinical complications in humans and has become a global threat. Therefore, this systematic review and meta-analysis was aimed to estimate the pooled prevalence of ESBL-producing Enterobacteriaceae in different clinical samples in Ethiopia.

METHODS

A systematic search was conducted on PubMed, Web of Science, Embase, Google Scholar and the Cochrane Library. All identified observational studies reporting the prevalence of ESBL-producing Enterobacteriaceae from clinical samples in Ethiopia were included. Four authors independently extracted data and analysed using R software version 3.6.1 and STATA statistical software version 13. A random-effects model was computed to estimate the pooled prevalence of ESBL-producing Enterobacteriaceae in Ethiopia.

RESULTS

Of 142 articles reviewed, 14 studies that fulfilled the inclusion criteria were included in the meta-analysis. The pooled prevalence of ESBL-producing Enterobacteriaceae in the different clinical specimens in Ethiopia was 49 % (95 % CI: 39, 60). Klebsiella pneumoniae was the leading ESBL-producing Enterobacteriaceae followed by Escherichia coli and Acinetobacter baumannii with a prevalence of 74, 67 and 60 %, respectively. ESBL-producing isolates showed a high rate of resistance to cefotaxime, ceftriaxone, ceftazidime, Amoxicillin clavulanic acid (AMC), ampicillin and aztreonam. The better options for the treatment of ESBL-producing Enterobacteriaceae are amikacin and Imipenem.

CONCLUSION

The magnitude of ESBL-producing Enterobacteriaceae in different clinical samples in Ethiopia is alarmingly high and represents a threat to human health. Hence, a coordinated effort needs to be implemented for the prevention and control of these Enterobacteriaceae .

In Vitro Efficacy of Flomoxef against Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Associated with Urinary Tract Infections in Malaysia

The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has greatly affected the clinical efficacy of β-lactam antibiotics in the management of urinary tract infections (UTIs). The limited treatment options have resulted in the increased use of carbapenem. However, flomoxef could be a potential carbapenem-sparing strategy for UTIs caused by ESBL-producers. Here, we compared the in vitro susceptibility of UTI-associated ESBL-producers to flomoxef and established β-lactam antibiotics. Fifty Escherichia coli and Klebsiella pneumoniae strains isolated from urine samples were subjected to broth microdilution assay, and the presence of ESBL genes was detected by polymerase chain reactions. High rates of resistance to amoxicillin-clavulanate (76–80%), ticarcillin-clavulanate (58–76%), and piperacillin-tazobactam (48–50%) were observed, indicated by high minimum inhibitory concentration (MIC) values (32 µg/mL to 128 µg/mL) for both species. The ESBL genes bla_CTX-M and bla_TEM were detected in both E. coli (58% and 54%, respectively) and K. pneumoniae (88% and 74%, respectively), whereas bla_SHV was found only in K. pneumoniae (94%). Carbapenems remained as the most effective antibiotics against ESBL-producing E. coli and K. pneumoniae associated with UTIs, followed by flomoxef and cephamycins. In conclusion, flomoxef may be a potential alternative to carbapenem for UTIs caused by ESBL-producers in Malaysia.

Prevalence and molecular characteristics of ESBL and AmpC β -lactamase producing Enterobacteriaceae strains isolated from UTIs in Egypt

BACKGROUND

Infections caused by Enterobacteriaceae are mainly treated with the β-lactam antibiotics, nevertheless, the emergence of species with plasmid-borne β-lactamases has decreased the efficacy of these antibiotics. Therefore, continuing studies on the resistance pattern of different regions is important for assessment of proper antimicrobial therapy protocols. The study aimed to characterize extended-spectrum β-lactamase (ESBL) and AmpC β -lactamase (AmpC) producing Enterobacteriaceae isolated from community-acquired UTIs in Egypt.

METHODS

Out of 705 urine samples, 440 Enterobacteriaceae isolates were investigated to detect ESBL and AmpC β -lactamases producers by phenotypic and molecular methods.

RESULTS

Out of 440 Enterobacteriaceae isolates, 311 were identified as ESBL producers by phenotypic testing. ESBL genes were detected in 308 isolates. BlaCTX-M-type was the most prevalent 254 (81.6%), out of them blaCTXM-15 was the commonest (152, 48.8%) followed by blaCTX-M-1 (140, 45%), blaCTX-M-8 (72, 23.1%) and lastly blaCTX-M-2 (4, 1.3%). blaTEM gene also was detected in a high rate (189, 60.7%). Two hundred and thirty-five (75.5%) of ESBL producers harbored blaCTX-M in combination with blaTEM and/or blaSHV genes. Multiple drug resistance in the ESBL-producers was significantly (P < 0.05) higher than in non-ESBL producers. Imipenem was the most effective drug against ESBL producers. Among 35 cefoxitin resistant isolates, 18 (51.4%) identified as carrying AmpC genes by multiplex PCR. Within AmpC β -lactamase genes, DHA gene was the predominant gene (15, 42.3%). CIT and MOX genes were also present, but in a low rate (5, 14.2% and 4, 11.4%) respectively. Co-existence of multiple AmpC genes was detected exclusively in K. pneumoniae isolates. E. coli isolates harbored DHA gene only. However, FOX gene was not detected in the study isolates. Seventeen of isolates carrying AmpC genes were also positive for ESBL genes.

CONCLUSION

The study shows that the prevalence of ESBL producing Enterobacteriaceae spread in south Egypt is alarming, however AmpC β -lactamase production is not so high.

Prevalence, phylogeny, and antimicrobial resistance of Escherichia coli pathotypes isolated from children less than 5 years old with community acquired- diarrhea in Upper Egypt

Background

Diarrhoea, affecting children in developing countries, is mainly caused by diarrheagenic Escherichia coli (DEC). This study principally aimed to determine the prevalence of DEC pathotypes and Extended-spectrum β-lactamase (ESBL) genes isolated from children under 5 years old with diarrhea.

Methods

A total of 320 diarrhoea stool samples were investigated. E. coli isolates were investigated for genes specific for enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and enterohemorrhagic E. coli (EHEC) using polymerase chain reaction (PCR). Furthermore, antimicrobial susceptibility testing, detection of antibiotic resistance-genes and phylogenetic typing were performed.

Results

Over all, DEC were isolated from 66/320 (20.6%) of the children with diarrhoea. EAEC was the predominant (47%), followed by typical EPEC (28.8%) and atypical EPEC (16.6%). Co-infection by EPEC and EAEC was detected in (7.6%) of isolates. However, ETEC, EIEC and EHEC were not detected. Phylogroup A (47%) and B2 (43.9%) were the predominant types. Multidrug-resistance (MDR) was found in 55% of DEC isolates. Extended-spectrum β-lactamase (ESBL) genes were detected in 24 isolates (24 blaTEM and 15 blaCTX-M-15). Only one isolate harbored AmpC β-lactamase gene (DHA gene).

Conclusion

The study concluded that, EAEC and EPEC are important causative agents of diarrhoea in children under 5 years. MDR among DEC has the potential to be a big concern.

Third-Generation Cephalosporin-Loaded Chitosan Used to Limit Microorganisms Resistance

From their discovery, antibiotics have significantly improved clinical treatments of infections, thus leading to diminishing morbidity and mortality in critical care patients, as well as surgical, transplant and other types of medical procedures. In contemporary medicine, a significant debate regarding the development of multi-drug resistance involves all types of pathogens, especially in acute care hospitals due to suboptimal or inappropriate therapy. The possibility of nanotechnology using nanoparticles as matrices to encapsulate a lot of active molecules should increase drug efficacy, limit adverse effects and be an alternative helping to combat antibiotic resistance. The major aim of this study was to obtain and to analyze physico-chemical features of chitosan used as a drug-delivery system in order to stop the antibiotic resistance of different pathogens. It is well known that World Health Organization stated that multidrug resistance is one of the most important health threats worldwide. In last few years, nano-medicine emerged as an improved therapy to combat antibiotic-resistant infections agents. This work relies on enhancement of the antimicrobial efficiency of ceftriaxone against gram(+) and gram(-) bacteria by antibiotic encapsulation into chitosan nanoparticles. Physicochemical features of ceftriaxone-loaded polymer nanoparticles were investigated by particle size distribution and zeta potential, Fourier-transform infrared spectroscopy (FTIR), Thermal Gravimetric Analysis (TG/TGA), Scanning Electron Microscopy (SEM) characteristics techniques. The obtained results revealed an average particle size of 250 nm and a zeta potential value of 38.5 mV. The release profile indicates an incipient drug deliverance of almost 15%, after 2 h of approximately 83%, followed by a slowed drug release up to 24 h. Characteristics peaks of chitosan were confirmed by FTIR spectra indicating a similar structure in the case of ceftriaxone-loaded chitosan nanoparticles. A good encapsulation of the antibiotic into chitosan nanoparticles was also provided by thermo-gravimetric analysis. Morphological characteristics shown by SEM micrographs exhibit spherical nanoparticles of 30-250 nm in size with agglomerated architectures. Chitosan, a natural polymer which is used to load different drugs, provides sustained and prolonged release of antibiotics at a specific target by possessing antimicrobial activity against gram(+) and gram(-) bacteria. In this research, ceftriaxone-loaded chitosan nanoparticles were investigated as a carrier in antibiotic delivery.

The Frequency and Antimicrobial Resistance of blaTEM and blaCTX-M Genes in Escherichia coli Isolated From Patients With a Urinary Tract Infection

Introduction: The production of β-lactamase in bacteria, especially in Escherichia coli as a prevalent opportunistic bacterium, has caused many problems in patient treatment. β-lactamases are encoded by extended-spectrum β-lactamase (ESBL) genes such as blaTEM and blaCTX-M. We aimed to assess the prevalence and antibiotic sensitivity of β-lactamases encoded by blaCTX-M and blaTEM in E. coli isolated from patients suffering from urinary tract infections (UTIs). Methods: Escherichia coli strains were isolated from the patients’ urine culture presented to medical diagnostic laboratories in Zabol, Iran. The agar disc-diffusion test was performed on Müller-Hinton agar to investigate the antibiotic resistance of these isolates using eight antimicrobial paper discs including gentamicin, tetracycline, co-trimoxazole, norfloxacin, cefuroxime, ampicillin, neomycin, and amoxicillin. A conventional polymerase chain reaction (PCR) was used to detect blaCTX-M and blaTEM. Results: The frequencies of resistance to cefuroxime, norfloxacin, co-trimoxazole, neomycin, amoxicillin, tetracycline, gentamicin, and ampicillin were found to be 45 (90%), 15 (30%), 33 (66%), 33 (66%), 44 (88%), 34 (68%), 4 (8%), and 50 (100%), respectively. Moreover, the prevalence of blaCTX-M was 25 (50%) while that of blaTEM was 16 (32%). Conclusion: Based on the results, gentamicin and norfloxacin can be recommended as effective antibacterials for treating UTI caused by E. coli in the study population. Moreover, the frequency of resistant genes including blaCTX-M and blaTEM was high in the isolated E. coli. Effective control systems including appropriate treatments for ESBL-producing strains are therefore required for humans and food animals.

Variations in the Morphology, Mechanics and Adhesion of Persister and Resister E. coli Cells in Response to Ampicillin: AFM Study

Persister bacterial cells are great at surviving antibiotics. The phenotypic means by which they do that are underexplored. As such, atomic force microscope (AFM) was used to quantify the contributions of the surface properties of the outer membrane of multidrug resistance (MDR)-Escherichia coli Strains (A5 and A9) in the presence of ampicillin at minimum inhibitory concentration (MIC) (resistant cells) and at 20× MIC (persistent cells). The properties quantified were morphology, root mean square (RMS) roughness, adhesion, elasticity, and bacterial surface biopolymers' thickness and grafting density. Compared to untreated cells, persister cells of E. coli A5 increased their RMS, adhesion, apparent grafting density, and elasticity by 1.2, 3.4, 2.0, and 3.3 folds, respectively, and decreased their surface area and brush thickness by 1.3 and 1.2 folds, respectively. Similarly, compared to untreated cells, persister cells of E. coli A9 increased their RMS, adhesion and elasticity by 1.6, 4.4, and 4.5 folds, respectively; decreased their surface area and brush thickness by 1.4 and 1.6 folds, respectively; and did not change their grafting densities. Our results indicate that resistant and persistent E. coli A5 cells battled ampicillin by decreasing their size and going through dormancy. The resistant E. coli A9 cells resisted ampicillin through elongation, increased surface area, and adhesion. In contrast, the persistent E. coli A9 cells resisted ampicillin through increased roughness, increased surface biopolymers' grafting densities, increased cellular elasticities, and decreased surface areas. Mechanistic insights into how the resistant and persistent E. coli cells respond to ampicillin's treatment are instrumental to guide design efforts exploring the development of new antibiotics or renovating the existing antibiotics that may kill persistent bacteria by combining more than one mechanism of action.

Risk Factors and Outcomes of Extended-Spectrum Beta-Lactamase-Producing E. Coli Peritonitis in Capd Patients

Objective

To determine the risk factors and outcomes of peritonitis caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in continuous ambulatory peritoneal dialysis (CAPD).

Patients and Methods

Episodes of E. coli CAPD peritonitis in our unit from October 1994 to August 2003 were reviewed. Demographic data, underlying medical conditions, recent use of gastric acid inhibitors (including H2 antagonist and proton pump inhibitor), recent antibiotic therapy, antibiotic regimen for peritonitis episodes, sensitivity test results of the E. coli isolated, and clinical outcomes were examined.

Results

Over a 10-year study period, 88 episodes of E. coli peritonitis were recorded; 11 of the 88 cases were caused by ESBL-producing E. coli. Recent use of cephalosporins and gastric acid inhibitor were associated with the development of ESBL-producing E. coli peritonitis. Compared with non-ESBL-producing E. coli peritonitis, more cases in the ESBL-producing E. coli group developed treatment failure (45.5% vs 13.0%, p = 0.02) and died of sepsis (27.3% vs 3.9%, p = 0.02). Peritoneal failure rate was higher in the ESBL-producing E. coli group, although the difference was not statistically significant (18.2% vs 3.9%, p = 0.12).

Conclusion

Peritonitis caused by ESBL-producing E. coli is associated with worse clinical outcomes. The use of cephalosporins and gastric acid inhibitors may contribute to its development. Further studies are warranted to investigate and determine the predisposing factors for ESBL-producing E. coli peritonitis.

Antibiotic Resistance Pattern and Frequency of PER-1, SHV-1 and AMPC Type B-Lactamase Genes in Pseudomonas aeruginosa Isolated from Clinical Samples

Background:

The existence of Extended Spectrum B-lactamase (ESBL) genes plays an important role in spreading B-lactam antibiotic resistance in the producing strains of these enzymes. The resistance of gram-negative bacteria, such as Pseudomonas aeruginosa, to different antimicrobial agents, especially B-lactams, has increasingly been reported.

Objective:

This study was conducted to determine the prevalence of TEM-1and VEB-1 beta-lactamases gene in P. aeruginosa isolates through Polymerase Chain Reaction (PCR) method.

Methods:

100 clinical isolates of P. aeruginosa were collected from different clinical samples. The antibiotic susceptibility was examined by the disc diffusion method. The presence of PER-1, SHV-1 and AMPC genes was detected by PCR method.

Results:

Out of the studied P. aeruginosa isolates, 7, 9 and 37 isolates were positive for PER-1, SHV-1 and AMPC B-lactamases resistance genes, respectively. Patients with urinary infection had the most resistant isolates. All isolates (100%) were sensitive to polymyxin B.

Conclusion:

Antibiotic resistance in isolates of Pseudomonas can be caused by B-lactamases resistance genes. Noticing the increasing rate of the ESBLs producing strains, using the appropriate treatment protocol based on the antibiogram pattern of the strains is highly recommended.

Carbapenemase and ESBL genes with class 1 integron among fermenting and nonfermenting bacteria isolated from water sources from India

The present study was aimed to detect the carbapenemase, extended-spectrum β-lactamase (ESBL), and intI1 gene of class 1 integron among fermenting (n = 61) and nonfermenting (n = 10) bacterial isolates recovered from water samples (n = 128). Isolates were identified by 16S rRNA sequencing. These isolates showed reduced-susceptibility to third-generation cephalosporins and carbapenems. The isolates varied in number and size of plasmids (2 kb to >20 kb). Plasmid DNA screening showed 5·6, 7, 11·2 and 26·7% prevalence of bla_KPC , bla_NDM , bla_SHV and bla_TEM genes respectively. Diverse bla_NDM (bla_NDM-1 and bla_NDM-4 ) and bla_SHV subtypes (bla_SHV-2 and bla_SHV-11 ) were recorded, unlike the single allelic bla_KPC (bla_KPC-2 ) and bla_TEM (bla_TEM-1 ) gene. Of the total 27 bla-gene-producing bacterial isolates, seven isolates co-harboured the carbapenemase genes (bla_NDM or bla_KPC or the both) along with the ESBL genes (bla_SHV or bla_TEM ). The intI1 gene of class 1 integron was detected among 12 (44·4%) of ESBL- and/or carbapenemase-harbouring isolates. Gene transferability was seen among four of the 10 Enterobacteriaceae donors. Carbapenemases and ESBLs with class 1 integron among aquatic environmental isolates raise the serious issue of the biosecurity and health of the ecosystem. SIGNIFICANCE AND IMPACT OF THE STUDY: Anthropologically affected and polluted environment harbours the resistance threats, where a diverse bacterial species maintain, develop and exchange genetic determinants that constitute a risk to human and ecological health. The antimicrobial resistance (AMR) in Enterobacteriaceae and non-Enterobacteriaceae bacteria caused the failure of the therapy of last resort (carbapenems) and thus lead to life-threatening infections affecting public health. Surveillance and monitoring of AMR could be important for epidemiological, diagnostic testing and control of pathogens. This is a point-prevalence study reporting the comparative occurrence and co-occurrence of carbapenemase and extended-spectrum β-lactamase genes among fermenting and nonfermenting bacteria isolated from the aquatic environment in India.

Changes in Cellular Elasticities and Conformational Properties of Bacterial Surface Biopolymers of Multidrug-Resistant Escherichia coli (MDR-E. coli) Strains in Response to Ampicillin

The roles of the thicknesses and grafting densities of the surface biopolymers of four multi-drug resistant (MDR) Escherichia coli bacterial strains that varied in their biofilm formation in controlling cellular elasticities after exposure to ampicillin were investigated using atomic force microscopy. Exposure to ampicillin was carried out at minimum inhibitory concentrations for different duration times. Our results indicated that the four strains resisted ampicillin through variable mechanisms. Strain A5 did not change its cellular properties upon exposure to ampicillin and as such resisted ampicillin through dormancy. Strain H5 increased its biopolymer brush thickness, adhesion and biofilm formation and kept its roughness, surface area and cell elasticity unchanged upon exposure to ampicillin. As such, this strain likely limits the diffusion of ampicillin by forming strong biofilms. At three hours’ exposure to ampicillin, strains D4 and A9 increased their roughness, surface areas, biofilm formation, and brush thicknesses and decreased their elasticities. Therefore, at short exposure times to ampicillin, these strains resisted ampicillin through forming strong biofilms that impede ampicillin diffusion. At eight hours’ exposure to ampicillin, strains D4 and A9 collapsed their biopolymers, increased their apparent grafting densities and increased their cellular elasticities. Therefore, at long exposure times to ampicillin, cells utilized their higher rigidity to reduce the diffusion of ampicillin into the cells. The findings of this study clearly point to the potential of using the nanoscale characterization of MDR bacterial properties as a means to monitor cell modifications that enhance “phenotypic antibiotic resistance”.

Extended-spectrum beta-lactamase production and multi-drug resistance among Enterobacteriaceae isolated in Addis Ababa, Ethiopia

Background

The global emergence and spread of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae have been threatening the ability to treat an infection. Hence, this study aimed to determine the prevalence of ESBL-producing and multi-drug resistance (MDR) Enterobacteriaceae (ESBLs-E) from different clinical specimens in Addis Ababa, Ethiopia.

Methods

A cross-sectional study was conducted from January 1 to May 30, 2017. A total of 426 Enterobacteriaceae isolates were identified from clinical specimens. The isolates were collected from four laboratories. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method on Muller Hinton agar (MHA). All Enterobacteriaceae were screened for ESBLs production using cefotaxime and ceftazidime as per CLSI guideline. Each ESBL screening positive Enterobacteriaceae were confirmed by a combination disk test (CDT). Data were entered and analyzed by using SPSS version-20.

Result

The most frequent Enterobacteriaceae were E. coli 228 (53.5%) and K. pneumoniae 103 (24.1%). The magnitude of ESBLs-E was 57.7% (246/426). The highest frequencies of ESBLs-E were observed in blood specimesns (84.4%) and the highest ESBLs production was observed in K. pneumoniae (85.4%). The highest resistance level was seen to sulfamethoxazole-trimethoprim (77.0%), amoxicillin with clavulanic acid (71.6%), cefotaxime (62.2%), cefepime (60.3%) and ceftazidime (60.8%). The overall magnitude of multi-drug resistance (MDR) level was 68.3%. Of ESBLs-E, 96.3% of them were MDR (P < 0.001).

Conclusion

There was a high prevalence of ESBLs-E and MDR isolate in Addis Ababa. Most of ESBLs-E was isolated primarily in blood and urine. The highest ESBLs production was observed among K. pneumoniae. Hence, strong infection control strategies must be implemented in hospital settings of the country.

The Effects of β-Lactam Antibiotics on Surface Modifications of Multidrug-Resistant Escherichia coli: A Multiscale Approach

Possible multidrug-resistant (MDR) mechanisms of four resistant strains of Escherichia coli to a model β-lactam, ampicillin, were investigated using contact angle measurements of wettability, crystal violet assays of permeability, biofilm formation, fluorescence imaging, and nanoscale analyses of dimensions, adherence, and roughness. Upon exposure to ampicillin, one of the resistant strains, E. coli A5, changed its phenotype from elliptical to spherical, maintained its roughness and biofilm formation abilities, decreased its length and surface area, maintained its cell wall integrity, increased its hydrophobicity, and decreased its nanoscale adhesion to a model surface of silicon nitride. Such modifications are suggested to allow these cells to conserve energy during metabolic dormancy. In comparison, resistant strains E. coli D4, A9, and H5 elongated their cells, increased their roughness, increased their nanoscale adhesion forces, became more hydrophilic, and increased their biofilm formation upon exposure to ampicillin. These results suggest that these strains resisted ampicillin through biofilm formation that possibly introduces diffusion limitations to antibiotics. Investigations of how MDR bacterial cells modify their surfaces in response to antibiotics can guide research efforts aimed at designing more effective antibiotics and new treatment strategies for MDR bacterial infections.

Antibiotic Susceptibility Patterns and Prevalence of Some Extended Spectrum Beta-Lactamases Genes in Gram-Negative Bacteria Isolated from Patients Infected with Urinary Tract Infections in Al-Najaf City, Iraq

BACKGROUND

Urinary Tract Infection (UTI) in patients with Chronic Kidney Disease (CKD) caused by multi-drug resistance and Extended Spectrum Beta Lactamase (ESBL)-producing gram-negative bacteria has been increased in different countries. The aim of the present study was to detect the antibiotic susceptibility patterns and the distribution of Bla-TEM, Bla-SHV and Bla-CTX-M genes in gram-negative bacteria isolated from outpatients infected with UTI, with and without CKD in Al-Najaf city, Iraq.

METHODS

A total of 120 non-duplicate urine samples were collected from outpatients (37 male and 83 female) infected with UTI in Al-Najaf city, Iraq; 60 samples from patients Without Kidney Disease (WKD) and 60 samples from patients with CKD. The antibiotic susceptibility testing was done according to Kirby-Bauer method. PCR technique was performed to investigate the prevalence of Bla-TEM, Bla-SHV and Bla-CTX-M genes.

RESULTS

A total of 126 different gram-negative bacterial strains were isolated. Escherichia coli (E. coli) was the most prevalent bacterium (49 isolates) followed by Idebsiella pneumonia (K. pneumonia) (35 isolates), Pseudomonas aeruginosa (P. aeruginosa) (18 isolates), Citrobacter freundii (C. freundii) (12 isolates), Enterobocter aerogenes (E. aerogenes) (8 isolates) and Proteus mirabilis (P. mirabilis) (4 isolates). All bacterial isolates from UTI patients with CKD were resistant to antibiotics and carried Bla-TEM, Bla-SHV and Bla-CTX-M genes more than isolates from UTI patients with WKD.

CONCLUSION

This study demonstrated that all bacterial isolates from UTI patients with CKD were more virulent than isolates from UTI patients with WKD.

Isolation of Extended-Spectrum β-lactamase- (ESBL-) Producing Escherichia coli and Klebsiella pneumoniae from Patients with Community-Onset Urinary Tract Infections in Jimma University Specialized Hospital, Southwest Ethiopia

Background

Klebsiella pneumoniae and Escherichia coli are the major extended-spectrum β-lactamase- (ESBL-) producing organisms increasingly isolated as causes of complicated urinary tract infections and remain an important cause of failure of therapy with cephalosporins and have serious infection control consequence.

Objective

To assess the prevalence and antibiotics resistance patterns of ESBL-producing Escherichia coli and Klebsiella pneumoniae from community-onset urinary tract infections in Jimma University Specialized hospital, Southwest Ethiopia, 2016.

Methodology

A hospital-based cross-sectional study was conducted, and a total of 342 urine samples were cultured on MacConkey agar for the detection of etiologic agents. Double-disk synergy (DDS) methods were used for detection of ESBL-producing strains. A disc of amoxicillin + clavulanic acid (20/10 µg) was placed in the center of the Mueller–Hinton agar plate, and cefotaxime (30 µg) and ceftazidime (30 µg) were placed at a distance of 20 mm (center to center) from the amoxicillin + clavulanic acid disc. Enhanced inhibition zone of any of the cephalosporin discs on the side facing amoxicillin + clavulanic acid was considered as ESBL producer.

Results

In the current study, ESBL-producing phenotypes were detected in 23% (n = 17) of urinary isolates, of which Escherichia coli accounts for 76.5% (n = 13) and K. pneumoniae for 23.5% (n = 4). ESBL-producing phenotypes showed high resistance to cefotaxime (100%), ceftriaxone (100%), and ceftazidime (70.6%), while both ESBL-producing and non-ESBL-producing isolates showed low resistance to amikacin (9.5%), and no resistance was seen with imipenem. In the risk factors analysis, previous antibiotic use more than two cycles in the previous year (odds ratio (OR), 6.238; 95% confidence interval (CI), 1.257–30.957; p = 0.025) and recurrent UTI more than two cycles in the last 6 months or more than three cycles in the last year (OR, 7.356; 95% CI, 1.429–37.867; p = 0.017) were found to be significantly associated with the ESBL-producing groups.

Conclusion

Extended-spectrum β-lactamases- (ESBL-)producing strain was detected in urinary tract isolates. The occurrence of multidrug resistance to the third-generation cephalosporins, aminoglycosides, fluoroquinolones, trimethoprim-sulfamethoxazole, and tetracyclines is more common among ESBL producers. Thus, detecting and reporting of ESBL-producing organisms have paramount importance in the clinical decision-making.

The 2017 Garrod Lecture: Genes, guts and globalization

The widespread use of antibacterial drugs over the last 70 years has brought immense benefits to human health at the price of increasing drug inefficacy. Antibacterial agents have a strong selective effect in both favouring resistant strains and allowing particular species and families of bacteria to prosper, especially in the healthcare setting. Whilst important Gram-positive bacterial pathogens such as Staphylococcus aureus and Streptococcus pneumoniae caused concern over the last 20 years because of the spread of antibiotic-resistant strains, Enterobacteriaceae have become the biggest challenge. They have very efficient mechanisms for genetic exchange, as illustrated by the emergence and rapid spread of CTX-M β-lactamases and the carbapenemases. The unique epidemiology of Enterobacteriaceae, with substantial numbers colonizing the mammalian gut and subsequent release into and spread in the environment, presents a significant threat to human health because of the high levels of exposure for the whole community. The use of antimicrobials in agriculture combined with global movements of people, animals and food, arising from worldwide industrialization, generates a diversity and level of resistance not seen previously. Control will require globally coordinated interventions similar to those needed to ameliorate climate change.

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene diversity and a higher plasmid burden than other Gram negative opportunists. Hence we propose it plays a key role in disseminating AMR genes from environmental microbes to clinically important pathogens.

Urosepsis Due to Extended-Spectrum β-Lactamase-Producing Escherichia coli: A Retrospective, Single-Centre Review of Risk Factors and Clinical Outcomes

BACKGROUND

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are pathogens that are implicated in urosepsis and may be associated with greater morbidity and mortality than non-ESBL Enterobacteriaceae. Identification of risk factors for ESBL infection may facilitate the selection of appropriate empiric therapy.

OBJECTIVES

The primary objectives were to determine the cumulative incidence of ESBL urosepsis, to identify major risk factors for ESBL urosepsis, and to determine the impact of international travel on development of ESBL urosepsis in an ethnically diverse Canadian population. The secondary objective was to characterize the outcomes of patients with ESBL urosepsis.

METHODS

A single-centre retrospective nested case-control study was conducted from January 2011 to June 2013. The study cohort consisted of adult patients with urosepsis and positive results on blood culture for ESBL-producing and non-ESBL-producing Enterobacteriaceae. Multivariate analysis was then used to determine risk factors for ESBL urosepsis.

RESULTS

The cumulative incidence of ESBL urosepsis at the study site was 19.4% (58/299) over 2.5 years. The 58 cases of ESBL urosepsis were compared with 118 controls (patients with urosepsis caused by non-ESBL Enterobacteriaceae). Significant predictors of ESBL urosepsis were chronic renal insufficiency (odds ratio [OR] 4.66, 95% confidence interval [CI] 1.96-11.08; p < 0.001) and travel to an endemic region in the previous 6 months (OR 4.62, 95% CI 1.17-18.19; p = 0.029), as well as Punjabi or Hindi as the primary language (OR 3.25, 95% CI 1.45-7.29; p = 0.004) and male sex (OR 2.65, 95% CI 1.21-5.80; p = 0.015). Patients with ESBL urosepsis had worse prognosis-in terms of death or discharge with palliative measures only-than those with non-ESBL urosepsis (7/58 [12.1%] versus 4/118 [3.4%]; p = 0.042).

CONCLUSIONS

Institution-specific data support prompt recognition of patients at risk for ESBL infections. Chronic renal insufficiency, recent travel to regions endemic for ESBL-producing organisms, primary language of Punjabi or Hindi, and male sex were the strongest risk factors for ESBL urosepsis at the study centre. However, findings from this single-centre study may not be generalizable to other institutions.

Imidazole decreases the ampicillin resistance of an Escherichia coli strain isolated from a cow with mastitis by inhibiting the function of autoinducer 2

Extended-spectrum β-lactamase-positive Escherichia coli is an important causative agent of mastitis in dairy cows that results in reduced milk production and quality, and is responsible for severe economic losses in the dairy industry worldwide. The quorum sensing signaling molecule autoinducer 2 (AI-2) is produced by many species of gram-negative and gram-positive bacteria, and might be a universal language for intraspecies and interspecies communication. Our previous work confirmed that exogenous AI-2 increases the antibiotic resistance of extended-spectrum β-lactamase-positive E. coli to the β-lactam group of antibiotics by upregulating the expression of the TEM-type β-lactamase. In addition, this regulation relies on the function of the intracellular AI-2 receptor LsrR. In the present work, we reported that exogenous imidazole, a furan carbocyclic analog of AI-2, decreases the antibiotic resistance of a clinical E. coli strain to β-lactam antibiotics by inhibiting the function of AI-2.

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical applications.

Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly, Clostridium difficile strains harboring this gene are at higher abundance in formula-fed infants than C. difficile strains lacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have higher replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data to five principal components classified by boosted decision trees. Among the genes involved in predicting whether an organism increased in relative abundance after treatment are those that encode subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics treatment and predict how organisms in the gut microbiome will respond to antibiotic administration.

IMPORTANCE The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical applications.

Pharmacophore-Based Repositioning of Approved Drugs as Novel Staphylococcus aureus NorA Efflux Pump Inhibitors

An intriguing opportunity to address antimicrobial resistance is represented by the inhibition of efflux pumps. Focusing on NorA, the most important efflux pump of Staphylococcus aureus, an efflux pump inhibitors (EPIs) library was used for ligand-based pharmacophore modeling studies. By exploitation of the obtained models, an in silico drug repositioning approach allowed for the identification of novel and potent NorA EPIs.

Isolation, Antimicrobial Susceptibility Profile and Detection of Sul1, blaTEM, and blaSHV in Amoxicillin-Clavulanate-Resistant Bacteria Isolated From Retail Sausages in Kampar, Malaysia

Background

Due to the overuse of antibiotics in livestock as a growth-promoting agent, the emergence of multi-antibiotic resistant bacteria is becoming a concern.

Objectives

In this study, we aimed to detect the presence and discover the molecular determinants of foodborne bacteria in retail sausages resistant towards the antibacterial agent amoxicillin-clavulanate.

Methods

Two grams of sausages were chopped into small pieces and transferred into sterile Luria-Bertani (LB) enrichment broths overnight before they were plated on MacConkey agar petri dishes. The bacteria isolated were then screened for amoxicillin-clavulanate resistance, and an antimicrobial susceptibility test of each isolate was performed by using the disc diffusion method. Double synergy and phenotypic tests were carried out to detect the presence of extended spectrum β-lactamase (ESBL). API 20E kit was used to identify the Enterobacteriaceae. All isolates were further examined by polymerase chain reaction (PCR) for resistant genes blaOXA-1, blaOXA-10, plasmid-mediated AmpC (blaCMY and blaDHA), and the chromosome-mediated AmpC, Sul1, blaTEM, and blaSHV genes.

Results

A total of 18 amoxicillin-clavulanate resistant isolates were obtained from seven different types of retail sausages. Only half of them were identified as Enterobacteriaceae, but none were ESBL-producers. All the 18 isolated strains demonstrated resistance towards amoxicillin-clavulanate, penicillin and oxacillin (100%), cefotaxime (71.4%), cefpodoxime (66.7%), and ampicillin (83.3%). blaTEM was the most frequently detected β-lactamase gene. Both plasmid- and chromosomal-bound blaTEM genes were detected in all of the isolated Enterobacteriaceae. blaSHV and Sul1 accounted for 22.2% and 11.1% of the amoxicillin-clavulanate resistant isolates, respectively, whereas blaAMPC, blaCMY, blaDHA, blaOXA-1, and blaOXA-10 were not found in any of the isolates. The only one ESBL-producing bacteria detected in this study was Chryseobacterium meningosepticum, which harbored the blaTEM gene.

Conclusions

The multidrug resistant bacteria that carry antibiotic resistant genes from retail sausages may increase the risk of transmission to humans via the consumption of contaminated sausages. Stricter measures must be taken to address the use of antibiotics in animal agriculture and to consider their potential impact on human health.

Prevalence of ESBL in Escherichia coli Isolates Among ICU Patients in a Tertiary Care Hospital

INTRODUCTION

Resistance to common antibiotics is a matter of grave concern in treating infections in hospital settings especially in Intensive Care Units (ICUs). One of the most commonly used and effective group of antibiotics, cephalosporins, exhibit resistance due to production of Extended Spectrum Beta- Lactamases (ESBLs). The prevalence of ESBL producing Escherichia coli (E.coli) has increased throughout the world and is a major cause of treatment failure in ICUs. As per our knowledge studies were not available on the prevalence of ESBL producing E.coli in ICUs of this region.

AIM

To determine the prevalence of ESBLs among Escherichia coli isolates in ICUs of a tertiary care hospital.

MATERIALS AND METHODS

A cross sectional study was conducted over a period of 4 years (Sept 2011 to Sept 2015) in the Department of Microbiology, Kalinga Institute of Medical Sciences (KIMS), Bhubaneswar. Consecutive non-duplicate isolates of E.coli recovered from 6800 clinical samples of patients admitted to different Intensive Care Units (ICUs) were subjected to ESBL screening test and then to CLSI recommended Phenotypic Confirmatory Disc Diffusion Tests (PCDDT) for ESBL production determination.

RESULTS

Out of 6800 samples, 1038 were E.coli isolates and 452(44%) were resistant to third generation cephalosporins. ESBL producing Escherichia coli among them were 276 (61.1%). Paediatric ICU showed the highest prevalence of ESBL E.coli at 80.9%. The highest prevalence of ESBL E.coli was in urine samples (82.6%) followed by pus (9.8%). The most effective antibiotic for ESBL producers was imipenem (96.7% sensitive), followed by amikacin (88.4%) and piperacillin- tazobactum (87%).

CONCLUSION

This study has highlighted the high prevalence of ESBL producing E.coli in the ICUs of our hospital. An in depth analysis of their antibiogram will be helpful in formulating the antibiotic policy and prevent spread of ESBL strains. It is recommended that ESBL testing should be done routinely to curtail antibiotic resistance and to effectively implement infection control measures.

Short communication: The role of autoinducer 2 (AI-2) on antibiotic resistance regulation in an Escherichia coli strain isolated from a dairy cow with mastitis

Extended spectrum β-lactamase (ESBL)-positive Escherichia coli is a major etiological organism responsible for bovine mastitis. The autoinducer 2 (AI-2) quorum sensing system is widely present in many species of gram-negative and gram-positive bacteria and has been proposed to be involved in interspecies communication. In E. coli model strains, the functional mechanisms of AI-2 have been well studied; however, in clinical antibiotic-resistant E. coli strains, whether AI-2 affects the expression of antibiotic resistance genes has not been reported. In this study, we report that exogenous AI-2 increased the antibiotic resistance of a clinical E. coli strain isolated from a dairy cow with mastitis by upregulating the expression of TEM-type enzyme in an LsrR (LuxS regulated repressor)-dependent manner.

Deacylation Mechanism and Kinetics of Acyl-Enzyme Complex of Class C β-Lactamase and Cephalothin

Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.

Effects of ceftiofur treatment on the susceptibility of commensal porcine E.coli--comparison between treated and untreated animals housed in the same stable

Background

Healthy farm animals have been found to act as a reservoir of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli). Therefore, the objective of the study was to determine the input of antimicrobial active ceftiofur metabolites in the stable via faeces and urine after intramuscular administration of the drug to pigs and the elucidation of the Escherichia coli ESBL resistance pattern of treated and untreated pigs housed in the same barn during therapy.

Methods

For determination of the minimal inhibitory concentration (MIC) the method of microdilutionaccording to the recommended procedure of the Clinical and Laboratory Standards Institute was used. Inaddition to that, a qualitative determination was performed by agar dilution. Unsusceptible E. coli speciesselected via agar dilution with cefotaxime were confirmed by MALDI-TOF and ESBL encoding genes wereidentified by PCR.

The amounts of ceftiofur measured as desfuroylceftiofur (DFC) in the different probes (plasma, urine, faeces and dust) were analysed by UPLC-MS/MS.

Results

In a first experiment two groups of pigs (6 animals per group) were housed in the same barn in two separated boxes. One group (group B) were treated with ceftiofur according to the licence (3 mg/kg administered intramuscularly (i.m.) on three consecutive days, day 1–3). During a second treatment period (day 29–31) an increased rate of ESBL resistant E. coli was detectable in these treated pigs and in the air of the stable. Moreover, the second group of animals (group A) formerly untreated but housed for the whole period in the same stable as the treated animals revealed increased resistance rates during their first treatment (day 45–47) with ceftiofur. In order to investigate the environmental input of ceftiofur during therapy and to simulate oral uptake of ceftiofur residues from the air of the stable a second set of experiments were performed. Pigs (6 animals) were treated with an interval of 2 weeks for 3 days with different doses of ceftiofur (3 mg/kg, 1 mg/kg and 0.3 mg/kg i.m.) as well as with 3 mg/kg per os) and the renal and biliary excretion of ceftiofur as its active metabolite were measured in comparison to the plasma levels. In addition to that, probes of the sedimentation dust and the air of the stable were analysed for drug residues.

Conclusion

The present study shows that treatment of several animals in a stable with ceftiofur influences the resistance pattern of intestinal Escherichia coli of the treated as well as untreated animals housed in the same stable. During therapy with the drug which was administered by injection according to the licence we detected nameable amounts of ceftiofur and its active metabolites in the dust and air of the stable.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-015-0578-3) contains supplementary material, which is available to authorized users.

Exploring the potential impact of an expanded genetic code on protein function

With few exceptions, all living organisms encode the same 20 canonical amino acids; however, it remains an open question whether organisms with additional amino acids beyond the common 20 might have an evolutionary advantage. Here, we begin to test that notion by making a large library of mutant enzymes in which 10 structurally distinct noncanonical amino acids were substituted at single sites randomly throughout TEM-1 β-lactamase. A screen for growth on the β-lactam antibiotic cephalexin afforded a unique p-acrylamido-phenylalanine (AcrF) mutation at Val-216 that leads to an increase in catalytic efficiency by increasing kcat, but not significantly affecting KM. To understand the structural basis for this enhanced activity, we solved the X-ray crystal structures of the ligand-free mutant enzyme and of the deacylation-defective wild-type and mutant cephalexin acyl-enzyme intermediates. These structures show that the Val-216-AcrF mutation leads to conformational changes in key active site residues-both in the free enzyme and upon formation of the acyl-enzyme intermediate-that lower the free energy of activation of the substrate transacylation reaction. The functional changes induced by this mutation could not be reproduced by substitution of any of the 20 canonical amino acids for Val-216, indicating that an expanded genetic code may offer novel solutions to proteins as they evolve new activities.

Community acquired multi-drug resistant clinical isolates of Escherichia coli in a tertiary care center of Nepal

Background

Multi-drug resistance (MDR) in Gram-negative organisms is an alarming problem in the world. MDR and extensively-drug resistance (XDR) is in increasing trend due to the production of different types of beta (β)-lactamases. Thus the aim of this study was to document the incidence of MDR and XDR in clinical isolates of Escherichia coli and also to find out the enzymatic mechanisms of β-lactam antibiotics resistance.

Methods

Two hundred clinical isolates of Escherichia coli (E. coli) identified by standard laboratory methods were studied. Antibiotic susceptibility profile was performed for all the isolates and the suspected isolates were phenotypically tested for the production of extended spectrum β-lactamase (ESBL), metallo β-lactamase (MBL) and AmpC β-lactamase (AmpC) by recommended methods.

Results

Around three-fourth (78%) of the total isolates were multi-drug resistant. ESBL, MBL and AmpC production was found in 24%, 15% and 9% of isolates respectively. Amikacin, chloramphenicol and colistin were found to be the most effective antibiotics.

Conclusions

High percentage of MDR was observed. β-lactamase mediated resistance was also high. Thus, regular surveillance of drug resistance due to β-lactamases production and infection control policy are of utmost importance to minimize the spread of resistant strains.

Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon

Objective: The emergence of extended-spectrum β-lactamase (ESBL)-producing bacteria is now a critical concern. The ESBL-producing Klebsiella pneumoniae constitutes one of the most common multidrug-resistant (MDR) groups of gram-negative bacteria involved in nosocomial infections worldwide. In this study we report on the molecular characterization through whole genome sequencing of an ESBL-producing K. pneumoniae strain, LAU-KP1, isolated from a stool sample from a patient admitted for a gastrointestinal procedure/surgery at the Lebanese Amrican University Medical Center-Rizk Hospital (LAUMCRH) in Lebanon.

Methods: Illumina paired-end libraries were prepared and sequenced, which resulted in 4,220,969 high-quality reads. All sequence processing and assembly were performed using the A5 assembly pipeline.

Results: The initial assembly produced 86 contigs, for which no scaffolding was obtained. The final collection of contigs was submitted to GenBank. The final draft genome sequence consists of a combined 5,632,663 bases with 57% G+C content. Automated annotation was performed using the RAST annotation server. Sequencing analysis revealed that the isolate harbored different β-lactamase genes, including bla_oxa−1, bla_CTX−M−15, bla_SHV−11, and bla_TEM−1b. The isolate was also characterized by the concomitant presence of other resistance determinants most notably acc(6′)-lb-cr and qnrb1. The entire plasmid content was also investigated and revealed homology with four major plasmids pKPN-IT, pBS512_2, pRSF1010_SL1344, and pKPN3.

Conclusions: The potential role of K. pneumonia as a reservoir for ESBL genes and other resistance determinants is along with the presence of key factors that favor the spread of antimicrobial resistance a clear cause of concern and the problem that Carbapenem-non-susceptible ESBL isolates are posing in hospitals should be reconsidered through systematic exploration and molecular characterization.

Amperometric detection of extended-spectrum β-lactamase activity: application to the characterization of resistant E. coli strains

The amperometric detection of extended-spectrum β-lactamase (ESBL) with carbon screen-printed sensors was investigated in the presence of the Nitrocefin, a commercially-available β-lactamase chromogenic cephalosporin substrate. Using an ESBL isolated from a clinical sample, it was shown for the first time that the intensity of a specific anodic pic current (EP = ∼+0.3 V vs. Ag/AgCl) resulting from the catalytic hydrolysis of the β-lactam ring was proportional to the amount of ESBL. The proof-of-principle of a novel susceptibility assay for the rapid and accurate identification of ESBL- producing bacteria was then demonstrated. The detection scheme relied on (i) the culture of the sample in a medium containing the cefotaxime supplemented or not with the clavulanic acid inhibitor to allow the specific determination of ESBL producers (ii) followed by the incubation of the bacteria with the Nitrocefin and (iii) the measurement of the enzyme product by cyclic voltammetry. The amperometric assay was further applied to the characterization of E. coli strains and to the quantification of the ESBL producers. A detection limit of 5 × 10(4) cfu mL(-1) ESBL-producing E. coli was achieved after a 10 min incubation time. In contrast to the approved routine assays, the electrochemical approach, which did not require isolated colonies to be performed, provided quantified results regarding ESBL activity within a few hours. Finally, owing to its cost-effectiveness, portability and simplicity, this test holds great promise for clinical and environmental applications.