Comparison of nine phenotypic methods for detection of extended-spectrum beta-lactamase production by Enterobacteriaceae

Investigation of plasmid-mediated quinolone resistance among extended-spectrum β-lactamase isolates of E. coli and K. pneumoniae

Escherichia coli and Klebsiella pneumoniae are important members of the Enterobacteriaceae family, involved in many infections. The increased resistance rate towards β-lactams and fluoroquinolones -which are the main therapeutic options- limits their treatment options. This study aimed to assess the local resistance patterns against different antimicrobials and to determine the extended-spectrum β-lactamase (ESBLs) producers. The study revealed that 36% of clinical isolates were ESBL producers, showing high resistance rates towards β-lactams and non-β-lactams, especially sulphamethoxazole-trimethoprim and fluoroquinolones. However, they were susceptible to chloramphenicol and doxycycline (33% and 20%; respectively). Also, the investigation aimed to screen the plasmid profile of quinolone-resistant ESBLs-producers and to detect the plasmid-mediated quinolone resistance genes including qnrA, qnrS, qnrB, qnrC, qnrD, and qnrVC. Moreover, the conjugative plasmid among the quinolone-resistant isolates was elucidated. The results showed that extracted plasmids of sizes ranging from ≈0.9 to 21.23 Kb, divided into 7 plasmid patterns were detected. A plasmid of approximately 21.23 Kb was found in all isolates and the QnrS gene was the most predominant gene. Moreover, the frequency of transconjugation within the same genus was higher than that recorded between different genera; where 68% of E. coli isolates transferred the resistance genes compared to Klebsiella isolates (36.6%). Plasmid profiles of transconjugants demonstrated great similarity, where 21.23 Kb plasmid was detected in all transconjugants. Since these transconjugants were quinolone-resistant ESBL producers, it has been suggested that quinolone resistance determinants might be carried on that plasmid.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Prevalence of blaCTX-M and blaTEM Genes in Cefotaxime-Resistant Escherichia coli Recovered from Tertiary Care at Central Nepal: A Descriptive Cross-Sectional Study

Urinary tract infections (UTIs) are highly prevalent globally, and various antibiotics are employed for their treatment. However, the emergence of drug-resistant uropathogens towards these antibiotics causes a high rate of morbidity and mortality. This study was conducted at the Microbiology Laboratory of Grande International Hospital from November 2021 to May 2022 and aimed to assess the prevalence of UTI caused by Escherichia coli and their antibiotic susceptibility pattern with a focus on extended-spectrum beta-lactamases (ESBLs) and the prevalence of two genes (blaCTX-M and blaTEM) in cephalosporin-resistant E. coli. Altogether, 1050 urine samples were processed to obtain 165 isolates of E. coli. The isolates were identified by colony morphology and biochemical characteristics. Antimicrobial susceptibility tests (ASTs) were determined by the Kirby-Bauer disk diffusion method, and their ESBL enzymes were estimated by the combined disk method (CDM). Two ESBL genes (blaCTX-M and blaTEM) were investigated by polymerase chain reaction (PCR) in cefotaxime-resistant E. coli. Among the 1050 urine samples that were processed, 335 (31.9%) were culture-positive with 165 (49.2%) identified as E. coli. The age group ≥60 years (30.3%) had greater susceptibility to bacterial infections. AST revealed that meropenem was highly effective (95.7% susceptibility), while ampicillin showed the least sensitivity (42.4%). Among the E. coli isolates, 86 were multidrug resistant (MDR) and 10 were extensively drug resistant (XDR). Of these, 46 MDR (96%) and 2 XDR (4%) were ESBL producers. The prevalence of ESBL genes (blaCTX-M and blaTEM) was 49.3% and 54.8%, respectively. The overall accuracy of CDM as compared to PCR for the detection of the blaCTX-M gene was 55.26%. The prevalence of MDR E. coli harboring the blaCTX-M and blaTEM genes underscores the imperative role of ESBL testing in accurately identifying both beta-lactamase producers and nonproducers.

Fecal Carriage of Extended-Spectrum β-Lactamase-/AmpC-Producing Escherichia coli in Pet and Stray Cats

Dogs have been reported as potential carriers of antimicrobial-resistant bacteria, but the role of cats has been poorly studied. The aim of this study was to investigate the presence and the risk factors associated with the fecal carriage of extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli (E. coli) in pet and stray cats. Fecal samples were collected between 2020 and 2022 from healthy and unhealthy cats and screened for ESBL/AmpC-producing E. coli using selective media. The presence of ESBL/AmpC-producing E. coli was confirmed by phenotypic and molecular methods. The evaluation of minimum inhibitory concentrations (MICs) was performed on positive isolates. Host and hospitalization data were analyzed to identify risk factors. A total of 97 cats' samples were collected, and ESBL/AmpC-producing E. coli were detected in 6/97 (6.2%), supported by the detection of blaCTX-M (100%), blaTEM (83.3%), and blaSHV (16.7%) genes and the overexpression of chromosomal ampC (1%). All E. coli isolates were categorized as multidrug-resistant. Unhealthy status and previous antibiotic therapy were significantly associated with ESBL/AmpC-producing E. coli fecal carriage. Our results suggest that cats may be carriers of ESBL/AmpC-producing E. coli, highlighting the need for antimicrobial stewardship in veterinary medicine and an antimicrobial-resistance surveillance program focusing on companion animals, including stray cats.

Phenotypic characterization and epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae strains from urinary tract infections in Garoua, Cameroon

Background and objectives

The emergence of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is causing increased morbidity and mortality around the world as a result of therapeutic failures. ESBL-E are priority pathogens due to their multidrug resistance (MDR). In Northern Cameroon, ESBL-producing bacteria, particularly in urinary tract infections (UTIs), are being increasingly isolated. This study aimed to retrospectively determine the prevalence of multi-drug resistant ESBL strains isolated from UTIs in Northern Cameroon and to evaluate the effectiveness of the ATB UR Gallery of BioMérieux in diagnosing ESBL-E in clinical settings.

Methods

Standard microbiology protocols and statistical tools were utilized to identify ESBL-producing bacteria and characterize their phenotypic susceptibility and resistance profiles in the study population.

Results

Out of the 144 enterobacteria isolates successfully cultured, 59 (41%) were identified as MDR strains. The ATB UR EU gallery identified 33 (23%) multi-drug resistant ESBL-producing strains, while the double synergy test identified 35 strains without disc reconciliation and 38 strains after reconciliation. The most prevalent ESBL-E isolate was Escherichia coli, accounting for 77.1% of the isolates, followed by Klebsiella pneumoniae (20%) and Enterobacter aerogenes (2.9%). Additionally, the study revealed the emergence of Imipenem resistance (5.7%), a critical last-resort antibiotic. However, all ESBL strains were sensitive to Fosfomycin (FSF/FOS), demonstrating its potential as an effective therapeutic option. Moreover, 37% of the ESBL producers exhibited co-resistance to over 20 different antibiotics.

Conclusion

This study provides valuable insights into the prevalence and susceptibility patterns of ESBL-E associated with UTIs in Northern Cameroon. These insights emphasizes the importance of implementing appropriate treatment guidelines and antimicrobial stewardship measures to mitigate the spread and impact of MDR ESBL-producing strains on public health.

Mortality difference from Klebsiella aerogenes vs Enterobacter cloacae bloodstream infections

Members of the order Enterobacterales, including Escherichia coli , Klebsiella species and Enterobacter species, are important pathogens in healthcare-associated infections. Higher mortality has been reported from infections due to Klebsiella pneumoniae than from E. coli , but prior studies comparing Enterobacter aerogenes (recently renamed Klebsiella aerogenes ) bacteraemia and Enterobacter cloacae complex bacteraemia have yielded conflicting results regarding whether clinical outcomes differ. We found bacteraemia with K. aerogenes was independently associated with greater risk of 30-day mortality than bacteraemia with Enterobacter cloacae complex.

Clinical outcome of wild-type AmpC-producing Enterobacterales infection in critically ill patients treated with β-lactams: a prospective multicenter study

Background

β-lactams are the main antibiotics used against wild-type AmpC-producing Enterobacterales (wtAE). However, they may fail or select AmpC-overproducing mutants. Our aim was to assess factors associated with clinical failure of β-lactams in the treatment of wtAE infection.

Methods

From September 2017 to December 2020, we prospectively included all consecutive patients treated by definitive β-lactams therapy for wtAE infection in four university ICUs. Clinical failure was defined as inadequate response to antimicrobial therapy leading to death or to the switch for a broader-spectrum antibiotic.

Results

177 patients were included and 29.4% progressed to clinical failure. E. cloacae was the most prevalent species (42.4%) and ventilator-associated pneumonia (VAP) was the most frequent wtAE infection (69.5%). Cefepime and cefotaxime were used as definitive antibiotic treatment in 42.9% and 27.7% of patients, respectively. Occurrence of AmpC-overproduction was documented in 5.6% of patients and was associated with clinical failure (p = 0.004). In multivariate analysis, VAP (p < 0.001, OR 11.58 [95% CI 3.11–43.02] and K. aerogenes (p = 0.030, OR 3.76 [95% CI 1.13–12.46]) were independently associated with clinical failure. Conversely, cefotaxime as definitive treatment was found inversely associated with the risk of clinical failure (p = 0.022, OR 0.25 [95% CI 0.08–0.82]). After inverse probability weighting, cefotaxime showed a 20% risk reduction of clinical failure (95% CI  5–35%, p = 0.007) whatever the location of infection, the SOFA score on the day of wtAE infection, or the bacterial species.

Conclusions

Clinical failure in the treatment of wtAE infections is associated with the infection site and the causal microorganism. Additionally, cefotaxime use is probably protective against clinical failure in wtAE infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13613-022-01079-5.

Investigating Antimicrobial Resistance and ESBL Producing Gene in Klebsiella Isolates among Neonates and Adolescents in Southern Bangladesh

Background

Multidrug-resistant (MDR) clones of Klebsiella pneumoniae (Kpn) have been increasingly documented in community-acquired and nosocomial infections all around the globe. Extended-spectrum β-lactamases (ESBLs) are a rapidly evolving group of β-lactamase enzymes derived from SHV genes by mutations. This research work aimed to investigate and analyze the widespread prevalence of Kpn antibiotic resistance in different areas of the southern part of Bangladesh.

Methods

This particular study was executed and implemented by using 501 clinical samples or isolates from two different hospitals in Chattogram. The disk diffusion method was used to detect Kpn's sensitivity to 16 antibiotics in a drug susceptibility test. By using the PCR technique, the widespread prevalence of antibiotic-resistant gene bla_SHV-11 was studied. Sequencing along with phylogenetic analysis was utilized to verify isolates with the bla_SHV-11 gene.

Results

Almost all of the Kpn isolates were spotted to be antibiotic-resistant. These Kpn isolates were resistant to β-lactams, aminoglycosides, and quinolones at high levels. The spatial analysis displayed that infections involving Kpn were more common in the urban areas (70%) than in the rural areas (30%). Neonates had substantially higher levels (p < 0.001) of resistance to multidrug than other age groups. Cefepime was identified as the most frequent antibiotic-resistant to all age groups (56.68%). The highest numbers of resistant isolates (36.92%) were found in urine samples. The ESBL gene bla_SHV-11 was found in 38% isolates.

Conclusion

The significant frequency of MDR Kpn harboring β-lactamases and AMR genes strongly suggests the requirement to develop effective antimicrobial resistance control and prevention measures in Bangladesh.

Effect of the Presence of Antibiotic Residues on the Microbiological Quality and Antimicrobial Resistance in Fresh Goat Meat

A total of 11 fresh goat legs were collected at the retail level. Mesophiles, Pseudomonas spp., Enterobacteriaceae, staphylococci, enterococci, Clostridium perfringens, Campylobacter spp., and Listeria monocytogenes counts were determined. Nine samples were free of antibiotic residues, while in the other two samples the presence of sulfadiazine and doxycycline was detected. The antimicrobial resistance of E. coli, staphylococci, Macrococcus spp., and enterococci isolates was also evaluated. Clostridium perfringens was found in two samples. Methicillin-resistant Staphylococcus aureus was detected in one sample. S. epidermidis isolated from one sample containing doxycycline residues showed resistance to mupirocin. Moreover, multi-resistant S. epidermidis and M. caseolyticus were found. Most of the isolated Enterococcus faecium were multi-resistant. Neither extended-spectrum β-lactamase -producing E. coli nor vancomycin-resistant enterococci were detected in any sample. The presence of doxycycline or sulfadiazine could affect the goat meat microbiota since less microbial diversity was found in these samples compared to those free of antibiotics. The presence of antibiotic residues could increase the antimicrobial resistance of enterococci in fresh goat meat. The presence of multidrug-resistant bacteria in goat meat could be considered a potential threat and should be monitored. Special measures should be taken at the farm level and during slaughter to reduce antimicrobial resistance.

Fully Automated EUCAST Rapid Antimicrobial Susceptibility Testing (RAST) from Positive Blood Cultures: Diagnostic Accuracy and Implementation

The objective of this study was to evaluate the accuracy and robustness of a fully automated EUCAST RAST (rapid antimicrobial susceptibility test) directly from positive blood culture and to appreciate its implementation constraints. This study was conducted in two phases: (i) spiked blood culture bottles (BCs) using 779 non-duplicate clinical isolates and (ii) a prospective clinical trial including 534 positive BCs sequentially processed in routine at the Bacteriology Laboratory of Geneva University Hospitals. The RAST results were assessed against EUCAST standardized disk diffusion testing results. Our first finding was that the results of the spiked BCs precisely predicted the clinical trial results. The overall categorical agreements for all species analyzed were greater than 95% at the different time points. RAST for Pseudomonas aeruginosa, however, raised several challenges. The categorical agreement for imipenem was lower than 95% at 6 h and was not improved with longer incubation times. Additionally, piperacillin-tazobactam, ceftazidime, and cefepime cannot be released at 6 h due to suboptimal performances, but the categorical agreement substantially improved at 8 h. Our results establish that the performance of fully automated EUCAST RAST directly from positive blood culture bottles is consistently robust, even for the detection of extended-spectrum β-lactamase (ESBL), carbapenemase-producing bacteria, and methicillin-resistant Staphylococcus aureus (MRSA). The automation markedly enhanced the percentage of readable inhibition zones and reduced the percentage of isolates categorized in the area of technical uncertainty (ATU). In summary, a fully automated EUCAST RAST can substantially improve laboratory workflow by reducing hands-on time and removing the strong constraints linked to manual read-outs at precisely defined times.

Phenotypic and genotypic detection of extended spectrum beta lactamase enzyme in Klebsiella pneumoniae

BACKGROUND

Klebsiella species are ubiquitous in nature and can be found in the natural environment and on mucosal surfaces of mammals and it is an important multidrug-resistant pathogen affecting humans and is a major source for hospital acquired infections. The aim of this study is to investigate the prevalence of ESBL enzyme among Klebsiella pneumoniae isolates by phenotypic methods from different hospital wards and detection of ESBL resistance genes such as TEM and SHV in Sulaimani city/ Kurdistan-Iraq.

METHODS

Klebsiella pneumoniae isolates were collected from different clinical samples from different hospitals, the isolates were identified by standard technique. Screening of ESBLs was undertaken by using double disk diffusion and standard disk diffusion methods. Real-time PCR was used for genotypic detection of TEM and SHV genes according to the standard protocol.

RESULT

Out of 54 Klebsiella pneumoniae isolates; 28 were ESBL positive, The pattern of antimicrobial susceptibility testing showed that the most resistant antibiotic are AMP (100%), AMC (100%) followed by CAZ (83.33%), CTX (75.9%), CPM (74%), ATM (70.37%). Both TEM and SHV genes were detected among 28 (51.85%) ESBL positive by using Real-time PCR method.

CONCLUSION

SHV gene was detected in most of the isolates of ESBL producers of Klebsiella pneumoniae.

Multidrug-Resistant Bacteria Isolated from Blood Culture Samples in a Moroccan Tertiary Hospital: True Bacteremia or Contamination?

Purpose

To demonstrate the relevance of clinico-biological correlation in the interpretation of positive blood cultures (BC) for multidrug-resistant (MDR) bacteria, among adult and pediatric patients, in order to distinguish between true bacteremia (TB) and contaminations and to evaluate the impact on patient management.

Patients and Methods

This six-month study was conducted at Mohammed VI University Hospital in Marrakech. All MDR bacteria isolated from BCs carried out on hospitalized patients during this period were included. For each positive BC to MDR microorganism, demographic and clinical characteristics, laboratory findings, therapeutic and evolution data were collected.

Results

TB was considered in 157 (94.6%) of the 166 positive-culture episodes for MDR bacteria, while 9 (5.4%) were classified as false-positive. Contamination rate was 0.2% (9/3824). TB and contaminations occurred mainly in intensive care units (ICUs), with the neonatal ICU being the most concerned (p = 0.016). Clinical signs of sepsis were present in all TB patients, with a significant difference between the two groups (p = 0.000). CRP values were higher in the TB group (p = 0.000). The most isolated true pathogens were ESBL-producing Enterobacterales (50%) and carbapenem-resistant Enterobacterales (33.3%). They also predominated in contaminated BCs. Isolation of the same microorganism from other sites was significantly associated with TB (p = 0.012). In contrast to the contaminations group, the difference in the clinical course of TB patients, according to whether or not they received appropriate probabilistic antibiotics, was statistically significant (p = 0.000). These patients had longer hospital stays and longer durations of antibiotic therapy. The overall mortality rate was 39.6%.

Conclusion

Distinguishing between MDR-positive BCs representing clinically significant bacteremia or simple contamination requires a careful clinical, biological, and microbiological confrontation of each MDR positive BC in order to avoid unnecessary overuse of broad-spectrum antibiotics and thus reduce resistance selective pressure.

Management of clinical infections of Escherichia coli by new β-lactam/β-lactamase inhibitor combinations

Background and Objectives

Escherichia coli (E. coli) is an important member of Enterobacteriaceae family involved in severe infections. The increased rate of resistance towards different classes of antibiotics limits their treatment options. The aim of this study was to assess the in vitro activity of classical and novel combinations of β-lactam/β-lactamase inhibitor against E. coli clinical isolates.

Materials and Methods

140 clinical isolates of E. coli were collected from clinical specimens from Gastrointestinal Surgery Center (GISC) in Egypt. Extended spectrum β-lactamase (ESBL) was detected by double disk synergy test. Furthermore, the minimum inhibitory concentrations (MICs) for five different combinations were determined using the broth microdilution method including: amoxicillin/clavulanate and ampicillin/sulbactam as an example for classical combinations and cefoperazone/sulbactam, ceftazidime/avibactam, and cefepime/enmetazobactam as an example for new combinations.

Results

The percentage of ESBL production among the tested isolates was 46.4%. Isolates were highly resistant to classical β-lactam/β-lactamase inhibitor combinations, where (40.7%) and (42.9%) of isolates were resistant to amoxicillin/clavulanate and ampicillin/sulbactam, respectively. While new β-lactam/β-lactamase inhibitor combinations had promising inhibitory action. The addition of novel β-lactamase inhibitors restored the susceptibility of isolates, where (94.3%) of isolates became susceptible to ceftazidime/avibactam combination, followed by cefoperazone/sulbactam (89.2%) and cefepime/enmetazobactam (85.7%). The synergistic effect seems to be effective where ceftazidime and avibactam were synergistic in 80% of isolates.

Conclusion

The antibacterial activity of some antimicrobial agents can be enhanced by the addition of new β-lactamase inhibitors. Further in vivo investigation is needed to confirm their therapeutic efficacy against local isolates.

Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods

Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.

Evaluation of three different methods for susceptibility testing of gentamicin in carbapenem resistant Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) have become a growing problem worldwide in recent years. Options for the treatment of CRE are limited and one of these options is gentamicin. For this reason, gentamicin susceptibility should be properly determined. In a recently reported study, it is recommended to review the results of automated systems for assessing gentamicin susceptibility in carbapenem-resistant isolates. In this study, we aimed to determine gentamicin susceptibility using three different methods and compare the methods. The study included 107 CRE isolates from different samples. Gentamicin susceptibility was determined using Vitek 2 Compact (bioMérieux, France), Microscan Walkaway Plus (Beckman Coulter, USA) automatic systems, and disk diffusion (DD) method. The broth microdilution method (BMD) was used as reference method. Minor, major, and very major errors and categorical agreement rates were determined for each method. Aminoglycoside-modifying enzymes (aac(6')Ib and aph(2″)Ia) were assayed in discrepant isolates. According to BMD results, 90.7%, 1,8 %, and 7.5 % of the isolates were determined as susceptible, intermediate, and resistant to gentamicin, respectively. Compared to the results of the BMD for detecting gentamicin susceptibility, disk diffusion method showed the highest categorical agreement (98.1%), and Vitek 2 Compact showed the lowest categorical agreement (90.6%). The very major error rates were determined 7.5%, 0.9%, and 0.9% for Vitek 2 Compact, Microscan Walkaway Plus, and DD method, respectively. In addition, aac(6')Ib and aph(2″)Ia genes were detected in 8 discrepant isolates. For gentamicin susceptibility, the DD showed the most compatible results. The DD can be used as a reliable method for determining gentamicin susceptibility. Compatibility of automated systems with BMD was acceptable, although lower than DD. The discrepancies detected in the Vitek 2 Compact results could be due to the presence of aac(6')Ib and/or aph(2″)Ia aminoglycoside-modifying enzymes.

Antibiotic Resistance Pattern of Extended Spectrum Beta Lactamase Producing Escherichia coli Isolated From Patients With Urinary Tract Infection in Morocco

Extended-spectrum β-lactamases producing Escherichia coli (ESBL-EC) lend resistance to most β-lactam antibiotics. Because of limited treatment options, ESBL-EC infections are generally more difficult to treat, leading to higher hospital costs, reduced rates of microbiological and clinical responses, and a threat to the patient’s life. This study aimed to determine the antibiotic resistance pattern of ESBL-EC isolated from patients with urinary tract infection in Morocco. This retrospective laboratory-based study was conducted at Cheikh Khalifa International University Hospital, Casablanca, from January 2016 to June 2019. A total of 670 urine samples were collected from urinary tract infection patients and processed by standard microbiological methods. In vitro susceptibility testing to different antibiotics of all identified isolates of Escherichia coli (E. coli) was performed following Kirby–Bauer’s disc diffusion method on Mueller–Hinton Agar according to the EUCAST standards. The reviewing of ESBL-EC was confirmed by the appearance of a characteristically shaped zone referred to as a “champagne cork” using the Combined Disk Test. Among a total of 438 E. coli isolated from nonrepetitive urine samples, two hundred fifty-nine (59%) were ESBL-EC, of which 200 (77%) were isolated from adult patients (over the age of 50) and the majority were female. All ESBL-EC isolates were resistant to third-generation cephalosporin and quinolones and sensitive to carbapenem and fosfomycin. Knowledge of antimicrobial resistance patterns in ESBL-EC, the major pathogen associated with urinary tract infection, is indispensable as a guide in choosing empirical antimicrobial treatment.

Isolation of third generation cephalosporin resistant Enterobacteriaceae from retail meats and detection of extended spectrum beta-lactamase activity

Various methods have been described to isolate third generation cephalosporin (3GC) resistant Enterobacteriaceae from foods, but it is not known how comparable they are between studies. Here, the performance of five enrichment broths and two selective agars are compared for their ability to isolate 3GC resistant Enterobacteriaceae from retail chicken, beef, pork, and veal samples. The results showed equivalence between Enterobacteriaceae enrichment broth (EE), lauryl sulfate broth (LST), and modified typtone soy broth (mTSB). Lower isolation rates were observed when LST and mTSB were supplemented with the 3GC antibiotic cefotaxime. The overall performance of MacConkey agar supplemented with cefotaxime and a proprietary selective agar (ESBL CHROMagar) was equivalent, although differences linked to the microbiota of specific meat commodities were noted. Regardless of the isolation method, further screening was required to confirm the taxonomy and resistance of the presumptive positive strains. Approximately 40% of confirmed 3GC resistant foodborne Enterobacteriaceae strains tested positive for extended spectrum beta-lactamase (ESBL) activity. Strains that were resistant to ceftriaxone and susceptible to cefoxitin were more likely to test positive for ESBL activity, as were strains that possessed either of two ESBL genes (bla_SHV or bla_TEM). Based on our results, we recommend using an antibiotic-free enrichment broth, two selective agars, and an isolate screening strategy to isolate 3GC resistant Enterobacteriaceae from retail meats. Antibiotic susceptibility testing and/or PCR screening for bla_SHV or bla_TEM can then be used to identify ESBL producing strains among the 3GC resistant meat isolates. The adoption of this approach by the research community will enable more effective monitoring of antibiotic resistance rates and trends among foodborne Enterobacteriaceae over time and across jurisdictions.

Performance of Fully Automated Antimicrobial Disk Diffusion Susceptibility Testing Using Copan WASP Colibri Coupled to the Radian In-Line Carousel and Expert System

The purpose of the present study was to assess the agreement at the categorical level between the Vitek 2 system and the Colibri coupled to the Radian under real routine laboratory conditions. The 675 nonduplicate clinical strains included in this study (249 Enterobacterales isolates, 198 Pseudomonas aeruginosa, 107 Staphylococcus aureus, 78 coagulase-negative staphylococci, 38 Enterococcus faecalis, and 5 Enterococcus faecium) were isolated from nonconsecutive clinical samples referred to our laboratory between June and November 2020. In addition, 43 carbapenemase-producing Enterobacterales (CPE) formerly identified and stored in our laboratory were added to the panel, for a total of 718 strains. The overall categorical agreements between the two compared methods were 99.3% (4,350/4,380; 95% CI 99% to 99.5%); 98.6% (2,147/2,178; 95% CI 98.0% to 99.0%); 99.4% (1,839/1,850; 95% CI 98.9% to 99.7%); and 99.4% (342/344; 95% CI 97.9% to 99.8%) for Enterobacterales, P. aeruginosa, Staphylococcus spp., and Enterococcus spp., respectively. The most important cause of the very major errors encountered on the Vitek 2 for P. aeruginosa (62%, 13/21) was related to the presence of heteroresistant populations. Among the 43 CPE included in this study, one OXA-48-like, and one OXA-181-like were missed by the Vitek 2, even by rigorously applying the CPE screening cutoffs defined by EUCAST. The Colibri coupled to the Radian provide a fully automated solution for antimicrobial disk diffusion susceptibility testing with an accuracy that is equal to or better than that of the Vitek 2 system.

Comparative Study of ESBL Production Among Uropathogenic Escherichia coli Clinical Isolates from Pre- and Post-menopausal Women in Egypt

Urinary tract infection (UTI) is regarded one of the most frequent bacterial infections in women. Accordingly, the aim of the current study was to determine the prevalence of extended-spectrum beta-lactamase (ESBL), as well as the degree of antimicrobial resistance among premenopausal (n = 44) and postmenopausal (n = 49) women suffering from uncomplicated UTI. Urinary samples (n = 93) collected from women with UTI were tested for their antimicrobial sensitivity and assessed for ESBL production by both phenotypic and genotypic methods. Phenotypically, the presence of ESBL was observed in 64 isolates, while polymerase chain reaction detected ESBL-encoding genes in 57 isolates. The CTX-M gene was the most predominant (51.6%), followed by TEM (46.2%), and the SHV gene (17.2%). Surprisingly, all ESBL-producing Escherichia coli isolates were multidrug-resistant (MDR). To the best of our knowledge, this is the first study conducted in Egypt showing significant correlation between ESBL production, multidrug resistance and menopausal state in women. The results demonstrate alarming signal for the dissemination of ESBL genes among uropathogenic E. coli that are MDR in Egypt.

Characterisation of ESKAPE Pathogens with Special Reference to Multidrug Resistance and Biofilm Production in a Nepalese Hospital

Background

“ESKAPE” is an acronym for a group of life-threatening nosocomial pathogens, viz, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. Global efforts on controlling multidrug-resistant (MDR) organisms have been hampered by their ability to escape antibacterial drugs. This study was undertaken to determine the prevalence of ESKAPE pathogens with prime focus on biofilm production and antibiotic resistance.

Methods

A total of 8756 clinical samples were processed for the isolation and identification of ESKAPE pathogens following standard microbiological procedures. These isolates were subjected to antimicrobial sensitivity test as per Clinical and Laboratory Standards Institute (CLSI) guidelines. Test for MDR, extended-spectrum β-lactamase (ESBL), metallo-β-lactamase (MBL), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE) was done by the disk diffusion and E-test methods. In the case of VRE molecular detection was done for vanA and vanB genes. All the isolates were processed for biofilm detection by the tube adherence method.

Results

The percentage distribution of Enterococcus faecium was 5.5%, S. aureus 33.4%, K. pneumoniae 33.0%, A. baumannii 8.6%, P. aeruginosa 18.6%, and Enterobacter aerogenes 0.9%. MRSA was 57.6%, and vancomycin resistance among Enterococcus faecium was 20%. ESBL- and MBL-producing K. pneumoniae were 16.1%, and 8.1%, A. baumannii 10.3% each and P. aeruginosa 10.7% and 8.3%, respectively. A total of 42.3% of isolates were biofilm producers. Linezolid was the drug of choice for VRE. Ampicillin-sulbactam was most useful against A. baumannii apart from polymyxins, whereas piperacillin-tazobactam was effective against other Gram-negative bacteria. VanA gene was detected in all the VRE isolates.

Conclusion

This study estimates the burden of the ESKAPE organisms and their antimicrobial resistance pattern in a hospital setting. A high percentage of drug resistance and biofilm production was noted; hence antimicrobial resistance surveillance targeting ESKAPE pathogens should be incorporated in the infection control policy in Nepal.

Adverse clinical outcomes associated with infections by Enterobacterales producing ESBL (ESBL-E): a systematic review and meta-analysis

OBJECTIVES

Enterobacterales producing ESBL (ESBL-E) have been notable for their rapid expansion in community settings. This systematic review and meta-analysis aimed to summarize evidence investigating the association between ESBL-E infection and adverse clinical outcomes, defined as bacteraemia, sepsis or septic shock, and all-cause mortality in adult patients.

METHODS

Database search was conducted in PubMed, Scopus and EMBASE. In general, studies were screened for effect estimates of ESBL-E colonization or infection on clinical outcomes with non-ESBL-producing Enterobacterales as comparator, adult populations and molecular ascertainment of ESBL gene. Meta-analysis was performed using the inverse variance heterogeneity model.

RESULTS

Eighteen studies were identified, including 1399 ESBL-E and 3200 non-ESBL-E infected patients. Sixteen of these studies included only bacteraemic patients. Mortality was studied in 17 studies and ESBL-E infection was significantly associated with higher odds of mortality compared with non-ESBL-producing Enterobacterales infection (OR = 1.70, 95% CI: 1.15-2.49, I 2=58.3%). However, statistical significance did not persist when adjusted estimates were pooled (aOR = 1.67, 95% CI: 0.52-5.39, I 2=78.1%). Septic shock was studied in seven studies and all included only bacteraemic patients. No association between ESBL-E infection and shock was found (OR = 1.23, 95% CI: 0.75-2.02, I 2=14.8%). Only one study investigated the association between ESBL-E infection and bacteraemia.

CONCLUSIONS

Infections by ESBL-E appear to be significantly associated with mortality but not septic shock. Available studies investigating bacteraemia and shock as an intermediate outcome of ESBL-E infections are lacking. Future studies investigating the relationship between clinical outcomes and molecular characteristics of resistant strains are further warranted, along with studies investigating this in non-bacteraemic patients.

Antibiotic resistance among Escherichia coli and Salmonella isolated from dairy cattle feces in Texas

In several developing countries, studies on antimicrobial resistance among bacteria from food animals are rare mostly because of under-resourced laboratories. The objective of this study was to develop and field-test a low cost protocol to estimate the isolate- and sample-level prevalence of resistance to critically important antibiotics among Escherichia coli and Salmonella isolated from dairy cattle feces. Using a predesigned protocol, fecal samples were collected to isolate non-type-specific E. coli and Salmonella using selective media without antibiotic supplements. Besides, samples were screened for E. coli and Salmonella isolates not susceptible to third-generation cephalosporins and quinolones using selective media supplemented with cefotaxime (1.0 μg/mL) and ciprofloxacine (0.5 μg/mL), respectively. All bacterial isolates were further tested for antibiotic susceptibility using disk diffusion. Bacterial isolates not susceptible to third-generation cephalosporins were tested for extended spectrum beta-lactamase (ESBL) phenotype using the combination disk test. Molecular methods were performed on selected bacterial isolates to identify and distinguish genetic determinants associated with the observed phenotypes. Among 85 non-type-specific E. coli isolated from MacConkey agar without antibiotics, the isolate-level prevalence of resistance to tetracycline was the highest (8.2%). Among 37 E. coli recovered from MacConkey agar with cefotaxime, 56.8% were resistant ceftriaxone. Among 22 E. coli isolates recovered from MacConkey agar with ciprofloxacin, 77.3% and 54.5% were resistant to nalidixic acid and ciprofloxacin, respectively. Sixteen Salmonella were isolated and only one demonstrated any resistance (i.e., single resistance to streptomycin). Among E. coli isolates not susceptible to ceftriaxone, an AmpC phenotype was more common than an ESBL phenotype (29 versus 10 isolates, respectively). Whole genome sequencing showed that phenotypic profiles of antibiotic resistance detected were generally substantiated by genotypic profiles. The tested protocol is suited to detecting and estimating prevalence of antimicrobial resistance in bacteria isolated from food animal feces in resource-limited laboratories in the developing world.

CON: Testing for ESBL production is unnecessary for ceftriaxone-resistant Enterobacterales

Phenotypic testing for Enterobacterales that harbour ESBLs is not additive to accurate in vitro β-lactam MICs for clinical decision-making. ESBL testing is an outdated practice established in an era of higher cephalosporin breakpoints to prevent resistant Enterobacterales carrying Ambler class A β-lactamases with affinity for later-generation β-lactams from being reported as susceptible to later-generation cephalosporins, leading to clinical failures. ESBL testing is problematic because of inaccuracies when multiple classes of β-lactamases are produced by the same organism, thus limiting the testing application to specific species and resistance types. Clinical laboratories should instead focus finite resources on accurate susceptibility testing using contemporary interpretative criteria to help guide therapeutic decisions. With continued emergence of antimicrobial resistance and in the setting of accurate susceptibility testing and current breakpoints the use of ESBL phenotypic testing is not helpful in clinical decision-making.

Non-carbapenem antimicrobial therapy in young infant with urinary tract infections caused by community-acquired extended-spectrum β-lactamase-producing Escherichia coli

BACKGROUND

The frequency of urinary tract infections (UTIs) caused by community-acquired extended-spectrum β-lactamase (CA-ESBL)-producing Enterobacteriaceae is increasing worldwide. Increased carbapenem use may lead to selection of carbapenem-resistant organisms, resulting in dire consequences for hospitals. We compared the outcomes of non-carbapenem antimicrobial therapy on UTIs caused by CA-ESBL-producing and non-producing Escherichia coli (E. coli) in infants younger than 6 months of age.

METHODS

We conducted a retrospective chart review, from January 2010 to December 2018, in infants (0-6 months old) with diagnosed UTIs caused by CA-ESBL-producing and non-producing E. coli at the Pusan National University Children's Hospital. Chart reviews were completed for patients whose urine sample had been collected using urinary catheterization. We treated all patients using non-carbapenem antimicrobials. Two weeks after therapy completion, clinical states were evaluated.

RESULTS

There were 105 and 582 patients diagnosed with UTIs caused by CA-ESBL-producing and non-producing E. coli, respectively. The mean age at diagnosis in ESBL and non-ESBL groups was 2.7 ± 1.6 and 2.8 ± 1.1 months (P = 0.711), respectively. There were no significant differences between ESBL and non-ESBL groups in the duration of fever (1.2 ± 0.5 and 1.2 ± 0.4 days, respectively, P = 0.761) or clinical cure states post therapy (101/105 and 567/582, respectively, P = 0.513).

CONCLUSION

This study found no significant differences in treatment outcomes between ESBL and non-ESBL groups treated with non-carbapenem antimicrobials. Therefore, initially administered non-carbapenem antimicrobials can be continued in patients with UTIs caused by CA-ESBL-producing E. coli who show clinical improvement.

Infectious Diseases Society of America Guidance on the Treatment of Extended-Spectrum β-lactamase Producing Enterobacterales (ESBL-E), Carbapenem-Resistant Enterobacterales (CRE), and Pseudomonas aeruginosa with Difficult-to-Treat Resistance (DTR-P. aeruginosa)

BACKGROUND

Antimicrobial-resistant infections are commonly encountered in US hospitals and result in significant morbidity and mortality. This guidance document provides recommendations for the treatment of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), carbapenem-resistant Enterobacterales (CRE), and Pseudomonas aeruginosa with difficult-to-treat resistance (DTR-P. aeruginosa).

METHODS

A panel of 6 infectious diseases specialists with expertise in managing antimicrobial-resistant infections formulated common questions regarding the treatment of ESBL-E, CRE, and DTR-P. aeruginosa infections. Based on review of the published literature and clinical experience, the panel provide recommendations and associated rationale for each recommendation. Because of significant differences in the molecular epidemiology of resistance and the availability of specific anti-infective agents globally, this document focuses on treatment of antimicrobial-resistant infections in the United States.

RESULTS

Approaches to empiric treatment selection, duration of therapy, and other management considerations are briefly discussed. The majority of guidance focuses on preferred and alternative treatment recommendations for antimicrobial-resistant infections, assuming that the causative organism has been identified and antibiotic susceptibility testing results are known. Treatment recommendations apply to both adults and children.

CONCLUSIONS

The field of antimicrobial resistance is dynamic and rapidly evolving, and the treatment of antimicrobial-resistant infections will continue to challenge clinicians. This guidance document is current as of 17 September 2020. Updates to this guidance document will occur periodically as new data emerge. Furthermore, the panel will expand recommendations to include other problematic gram-negative pathogens in future versions. The most current version of the guidance including the date of publication can be found at www.idsociety.org/practice-guideline/amr-guidance/.

Risk Factors and Impact of Perioperative Prophylaxis on the Risk of Extended-spectrum β-Lactamase-producing Enterobacteriaceae-related Infection Among Carriers Following Liver Transplantation

BACKGROUND

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) carriage is frequent among liver transplant (LT) recipients, thereby fostering a large empirical carbapenem prescription. However, ESBL-E infections occur in only 10%-25% of critically ill patients with rectal colonization. Our aim was to identify risk factors for post-LT ESBL-E infection in colonized patients. The effect of perioperative antimicrobial prophylaxis (AP) was also analyzed in patients with prophylaxis lasting <48 hours and without proven intraoperative infection.

METHODS

Retrospective study from a prospective database including patients with a positive ESBL-E rectal screening transplanted between 2010 and 2016.

RESULTS

Among the 749 patients transplanted, 100 (13.3%) were colonized with an ESBL-E strain. Thirty-nine (39%) patients developed an infection related to the same ESBL-E (10 pulmonary, 11 surgical site, 13 urinary, 5 bloodstream) within 11 postoperative days in median. Klebsiella pneumoniae carriage, model for end-stage liver disease ≥25, preoperative spontaneous bacterial peritonitis prophylaxis, and antimicrobial exposure during the previous month were independent predictors of ESBL-E infection. We propose a colonization to infection risk score built on these variables. The prevalence of infection for colonization to infection score of 0, 1, 2, and ≥3 were 7.4%, 26.3%, 61.9%, and 91.3%, respectively. Of note, the incidence of post-LT ESBL-E infection was lower in case of perioperative AP targeting colonizing ESBL-E (P = 0.04).

CONCLUSIONS

Thirty-nine percentage of ESBL-E carriers develop a related infection after LT. We identified predictors for ESBL-E infection in carriers that may help in rationalizing carbapenem prescription. Perioperative AP targeting colonizing ESBL-E may be associated with a reduced risk of post-LT ESBL-E infections.

Efficacy of β-lactam/β-lactamase inhibitors to treat extended-spectrum beta-lactamase-producing Enterobacterales bacteremia secondary to urinary tract infection in kidney transplant recipients (INCREMENT-SOT Project)

BACKGROUND

Whether active therapy with β-lactam/β-lactamase inhibitors (BLBLI) is as affective as carbapenems for extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) bloodstream infection (BSI) secondary to urinary tract infection (UTI) in kidney transplant recipients (KTRs) remains unclear.

METHODS

We retrospectively evaluated 306 KTR admitted to 30 centers from January 2014 to October 2016. Therapeutic failure (lack of cure or clinical improvement and/or death from any cause) at days 7 and 30 from ESBL-E BSI onset was the primary and secondary study outcomes, respectively.

RESULTS

Therapeutic failure at days 7 and 30 occurred in 8.2% (25/306) and 13.4% (41/306) of patients. Hospital-acquired BSI (adjusted OR [aOR]: 4.10; 95% confidence interval [CI]: 1.50-11.20) and Pitt score (aOR: 1.47; 95% CI: 1.21-1.77) were independently associated with therapeutic failure at day 7. Age-adjusted Charlson Index (aOR: 1.25; 95% CI: 1.05-1.48), Pitt score (aOR: 1.72; 95% CI: 1.35-2.17), and lymphocyte count ≤500 cells/μL at presentation (aOR: 3.16; 95% CI: 1.42-7.06) predicted therapeutic failure at day 30. Carbapenem monotherapy (68.6%, primarily meropenem) was the most frequent active therapy, followed by BLBLI monotherapy (10.8%, mostly piperacillin-tazobactam). Propensity score (PS)-adjusted models revealed no significant impact of the choice of active therapy (carbapenem-containing vs any other regimen, BLBLI- vs carbapenem-based monotherapy) within the first 72 hours on any of the study outcomes.

CONCLUSIONS

Our data suggest that active therapy based on BLBLI may be as effective as carbapenem-containing regimens for ESBL-E BSI secondary to UTI in the specific population of KTR. Potential residual confounding and unpowered sample size cannot be excluded (ClinicalTrials.gov identifier: NCT02852902).

Review of phenotypic assays for detection of extended-spectrum β-lactamases and carbapenemases: a microbiology laboratory bench guide

Background

Infections caused by gram-negative antibiotic-resistant bacteria continue to increase. Despite recommendations by the Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) with regards to detection of antibiotic degrading enzymes secreted by these bacteria, the true prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase producers remains a difficult task to resolve. Describing of previously designed phenotypic detection assays for ESBLs and carbapenemases in a single document avails a summary that allows for multiple testing which increases the sensitivity and specificity of detection.

Methods and aims

This review, therefore, defined and classified ESBLs and carbapenemases, and also briefly described how the several previously designed phenotypic detection assays for the same should be performed.

Conclusion

Extended-spectrum β-lactamase and carbapenemase detection assays, once performed correctly, can precisely discriminate between bacteria producing these enzymes and those with other mechanisms of resistance to β-lactam antibiotics.

Temocillin breakpoints in pyelonephritis: evaluation in a murine model due to ESBL-producing Escherichia coli clinical isolates

BACKGROUND

Due to a spectrum restricted to Enterobacteriaceae and stability against ESBL and AmpC enzymes, temocillin is of major interest for the treatment of pyelonephritis. But there are still uncertainties about the optimal regimen and clinical breakpoints.

OBJECTIVES

To study in a murine model of pyelonephritis the activity of temocillin against Escherichia coli isolates with different MICs in order to evaluate clinical breakpoints.

METHODS

Four clinical uropathogenic E. coli isolates with temocillin MICs of 8 mg/L (Ec8), 16 mg/L (Ec16), 32 mg/L (Ec32) and 64 mg/L (Ec64) were evaluated. Antibiotic 24 h T>MIC achieved in humans was reproduced in mice with either intravenous temocillin (2 g q12h or 2 g q8h) or intravenous imipenem (1 g q8h). Efficacy was assessed by bacterial count in kidneys.

RESULTS

Compared with controls, temocillin at 2 g q12h was highly efficient against Ec8 (-3.32 log10 cfu/g and negative cultures in 93% of mice; P < 0.001); imipenem gave similar results. Temocillin at 2 g q12h also induced high reduction of bacterial count against Ec16 (-2.92 log10 cfu/g; P < 0.001), albeit cultures were negative in only 48% of mice. In contrast, no significant effect was observed in mice infected by Ec32 (-0.01 log10 cfu/g; P = 0.981) or Ec64 (-0.55 log10 cfu/g; P = 0.523). Even temocillin at 2 g q8h failed to control Ec32 infection (-1.55 log10 cfu/g; P = 0.197).

CONCLUSIONS

This model suggests a clinical breakpoint up to 16 mg/L for non-severe pyelonephritis treated with temocillin at 2 g q12h, a value consistent with the few previous available data.

A systematic review on the prevalence of extended-spectrum beta lactamase-producing Gram-negative bacteria in Nigeria

OBJECTIVE

There are numerous reported cases of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae in Nigeria. Yet, there are regions in Nigeria where cases of ESBL were under-reported. The review aims to assess the prevalence of ESBL-producing Gram-negative bacteria in Nigeria and the genes involved.

METHODS

An extensive literature search was carried out through an electronic database including PubMed, Scopus, Google Scholar and African Journals Online (AJOL). Articles published between January 2004 and November 2019 were included in the study. The titles and abstracts of the retrieved articles were reviewed, and then the full texts of the selected articles were reviewed. Articles were divided according to geopolitical zones.

RESULTS

Among the 217 articles identified, 60 studies (10 from north-central, 4 from northeast, 7 from the northwest, 17 from the southeast, 10 from south-south, and 12 from southwest Nigeria) were included. The highest prevalence recorded was 82.3%, while the lowest was 7.5%. The genes TEM, SHV, and CTX-M were the predominant variant commonly found. The most frequently used phenotypic detection method is the double disc synergy test (DDST).

CONCLUSION

ESBL-producing Gram-negative bacteria in hospital and community settings in Nigeria were commonly found. The prevalence of ESBL is very high, with one of the geopolitical zones under-reported. Future research should be conducted in these zones where there are scant studies, and a holistic approach involving the clinicians, researchers, laboratory scientists, and patients will go a long way in reducing the dissemination of this resistance mechanism.

Combined Molecular and Phenotypic Antimicrobial Susceptibility Testing Is Beneficial in Detection of ESBL and AmpC Beta-Lactamase Producing Isolates of Enterobacteriaceae in Pediatric Patients with Bloodstream Infections

Objectives: The aim was to assess the potential advantage of combined genotypic testing with phenotypic antimicrobial susceptibility testing (AST) to detect AmpC β-lactamases (AmpC) and extended-spectrum β-lactamases (ESBL) producing Enterobacteriaceae isolated from blood cultures in a pediatric population. Materials and Methods: All first-time Enterobacteriaceae isolates recovered from blood cultures of pediatric patients at the Cincinnati Children's Hospital Medical Center between January 2017 and December 2018 were evaluated. The Check-MDR CT103XL β-lactamase assay was used to determine the presence of AmpC and ESBL, while AST was performed using the VITEK 2 platform. Phenotypic ESBL resistance was defined by resistance to either ceftriaxone or ceftazidime using Clinical and Laboratory Standards Institute breakpoints, while combined cefoxitin resistance with ceftriaxone or ceftazidime resistance was used to detect AmpCs (as per European Committee on Antimicrobial Susceptibility Testing standards). Results: Overall, there were 170 isolates. Genotypically, 21 (12.4%) had AmpC and 18 (10.6%) had ESBL genes detected. Phenotypically, 11 (6.5%) isolates were AmpC and 26 (15.3%) were ESBL producing organisms. Genotypic testing identified an additional 14 AmpC and two ESBL isolates that failed to meet phenotypic criteria. Conclusions: Using combined genotypic and phenotypic methods to detect AmpC and ESBL producing organisms increased the identification of resistant organism and provided potentially clinical relevant data to guide the treatment of resistant organisms.

Distribution of genes encoding adhesins and biofilm formation capacity among Uropathogenic Escherichia coli isolates in relation to the antimicrobial resistance

Background

Escherichia coli is the most predominant pathogen involved in UTIs. Mainly, fimbrial surface appendages are implicated in adherence to urothelium besides non-fimbrial proteins.

Objectives

to determine prevalence of genes encoding fimbrial and non-fimbrial proteins among Uropathogenic Escherichia coli (UPEC). Furthermore, distribution of these genes and biofilm formation capacity were investigated in relation to antimicrobial resistance.

Methods

Antimicrobial susceptibility of 112 UPEC isolates was performed using disc diffusion method. ESBL production was confirmed by double disc synergy test. Genes encoding fimbrial and non-fimbrial proteins were detected using PCR and biofilm formation was investigated using microtitre plate assay.

Results

UPEC isolates exhibited high resistance against doxycyclines (88.39 %), β-lactams (7.14–86.6%), sulphamethoxazole-trimethoprim (53.75%) and fluoro-quinolones (50%). Fifty percent of tested isolates were ESBL producers. PapGII gene was statistically more prevalent among pyelonephritis isolates. SfaS, focG and picU genes were statistically associated with fluoroquinolone (FQs) sensitive isolates and Dr/afaBC gene was statistically associated with ESBL production. Moreover, non-MDR isolates produced sturdier biofilm.

Conclusion

PapGII adhesin variant seems to have a critical role in colonization of upper urinary tract. There is a possible link between antimicrobial resistance and virulence being capable of affecting the distribution of some genes besides its negative impact on biofilm formation.

Temocillin against Enterobacteriaceae isolates from community-acquired urinary tract infections: low rate of resistance and good accuracy of routine susceptibility testing methods

Background

Temocillin is an old 'revived' antibiotic that may play an important role in the treatment of febrile urinary tract infection (UTI). Data regarding its activity against current Enterobacteriaceae isolates as well as the performance of routine susceptibility testing methods are, however, scarce.

Objectives

To determine the MICs of temocillin for Enterobacteriaceae strains reflecting the current epidemiology and to analyse the accuracy of three commercial methods.

Methods

Enterobacteriaceae isolates causing community-acquired UTI were prospectively collected from September 2015 to January 2017 in two French centres. Temocillin MIC was determined by agar dilution (AD) as the reference method and then compared with: (i) susceptibility testing by disc diffusion; (ii) MIC determination by Etest; and (iii) MIC estimation by the Vitek 2 automated system.

Results

A total of 762 Enterobacteriaceae were analysed comprising 658 (86.4%) Escherichia coli and 37 (4.9%) ESBL-producing isolates. Susceptibility rate assessed by AD was 99.6% according to the 8 mg/L clinical breakpoint and was significantly lower against the ESBL-producing isolates than the non-ESBL-producing isolates (94.6% versus 99.9%, P < 0.01). The MIC50 and MIC90 for the total set were 3 and 6 mg/L, respectively. According to the 8 mg/L clinical breakpoint, the major error rate was <1% for disc diffusion and Etest, and significantly higher for Vitek 2 (4.3%, P < 0.01), but still low. No very major error was noticed.

Conclusions

Temocillin showed a high level of activity against Enterobacteriaceae from community-acquired UTI and good to excellent reliability of routine methods for susceptibility testing in such a setting.

Prevalence, Antibiogram, and Resistance Profile of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates from Pig Farms in Luzon, Philippines

This cross-sectional study was conducted to determine the prevalence, antibiogram, and resistance profile of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) isolates from healthy pigs and pig farms in Luzon, Philippines. A total of 162 rectal samples from healthy finisher and breeder pigs and boot swab samples from pig houses were collected from 54 randomly selected pig farms. Bacteria were isolated and screened using MacConkey agar plate supplemented with 1 mg/L cefotaxime. Identification of bacteria and antimicrobial susceptibility test were carried out through Vitek^® 2 and combined disk test. PCR amplifications were carried out in all isolates targeting bla_CTX-M and its five major groupings, bla_TEM, and bla_SHV. The farm prevalence of ESBL-EC was 57.41% (95% confidence interval [CI] = 43.21-70.77). A total of 48 (29.63%) ESBL-EC isolates were isolated from samples that showed 14 different phenotypic multidrug resistance patterns. The prevalence of bla_CTX-M gene was 91.67% (95% CI = 80.02-97.68). All major bla_CTX-M-groups except bla_{CTX-M-25group} were detected. The bla_CTX-M-1 was the most prevalent bla_CTX-M gene, 75.0% (95% CI = 60.40-86.36). The prevalence of bla_TEM and bla_SHV genes was 91.67% (95% CI = 80.02-97.68) and 60.42% (95% CI = 45.27-74.23), respectively. Coexistence of different bla_CTX-M, bla_TEM, and bla_SHV genes was observed in 44 isolates with 20 different genotypic patterns. High prevalence, diverse antibiogram profile, and genotypic resistance pattern of ESBL-EC isolates from healthy pigs and pig farms were observed in this study that could result in possible transmission to farm workers, susceptible bacteria, and the environment.

Virulence and Antibiotic Resistance Patterns in E. coli, Morocco

Of 28 non-duplicate isolates of Escherichia coli recovered from yellow-legged Larus michahellis in Morocco, 92.86% were resistant to more than three antibiotics and 71.4% were multidrug resistant. Phylogenetic group A was most predominant (57.14%), followed by B1 (18%), B2 (14.28%) and F (10.71%). One isolate was resistant to ertapenem and contained the bla_OXA-48 gene. The plasmid-mediated quinolone resistance determinants were detected in nine isolates (aac(6')-Ib-cr, qnrS1, qnrB1). Thirteen isolates carried one of the Shiga toxin E. coli-associated genes: stx1 (n = 6), stx2 (n = 5) and eae (n = 2) genes. Our data support the idea that gull feces may create potential public health risk.

Synergistic in vitro activity between aztreonam and amoxicillin-clavulanate against Enterobacteriaceae-producing class B and/or class D carbapenemases with or without extended-spectrum β-lactamases

Introduction. Carbapenemase-producing Enterobacteriaceae have become a major public health concern over the last decade and treatment options are limited.Aims. We evaluated the synergistic activity of the combination of aztreonam (ATM) and clavulanate for 41 β-lactam-resistant clinical isolates harbouring class B or/and class D carbapenemases combined or not with extended-spectrum β-lactamases (ESBLs).Methodology. The MICs of ATM, with and without amoxicillin-clavulanate (AMC), were determined. Time-kill assays were performed for three representative strains.Results. The ATM-AMC combination had a synergistic effect on 34/41 (83 %) isolates. The MIC of ATM, in the presence of clavulanate, was ≤1 mg l^-1 for 15/41 (37 %) isolates and ≤4 mg l^-1 for 29/41 (71 %) isolates. Synergistic activity was observed for 34/37 (92 %) isolates producing ESBLs and carbapenemases, compared to 0/4 (0 %) for ESBL-negative strains. Complete or partial bactericidal activity was obtained when the MIC of the combination was 0.5 mg l^-1 and 1.5 mg l^-1 or 8 mg l^-1, respectively.Conclusion. The combination of ATM and AMC could be an attractive unconventional treatment for infections due to carbapenemase- and ESBL-producing Enterobacteriaceae.

Effective Oral Combination Treatment for Extended-Spectrum Beta-Lactamase-Producing Escherichia coli

Background: Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) is increasing worldwide. The drugs of choice for treatment of ESBLs are parenteral carbapenems. The aim of this study was to evaluate the in vitro and in vivo efficacy of a new combination of oral cephalosporins and amoxicillin/clavulanate in treatment of ESBL-EC. Methods: A total of 150 ESBL-EC samples were collected over 1 year from two referral centers. Synergistic studies of cephalosporins and amoxicillin/clavulanate were performed in vitro using disk approximation and disk replacement methods. Combination treatment was assessed in vivo on 20 ESBL-EC urinary tract infection (UTI) patients. Results: ESBL-EC isolates were confirmed in 150 patients with a mean age of 46.67 years, 75.2% of them being women. Antibiotic susceptibility testing of isolates indicated high resistance rate to oral antibiotics. The frequency of positive synergy and mean distance of synergy between cephalosporins and amoxicillin/clavulanate was significantly higher with cefotaxime and cefixime compared with cefpodoxime, cefdinir, and ceftazidime using disk approximation and disk replacement methods (p < 0.05). Addition of amoxicillin/clavulanate enhanced the susceptibility rate with cefixime from 8.6% to 86.3%, significantly higher than with other cephalosporins (p < 0.0005). Cefixime and amoxicillin/clavulanate synergy was not affected by age, gender, hospital, department, sample type, or bacterial load. Eighteen of 20 ESBL-EC-positive UTI patients had a positive in vitro synergy test and complete clinical and microbiological resolution after completion of cefixime and amoxicillin/clavulanate oral treatment course. Conclusions: Cefixime and amoxicillin/clavulanate combination therapy could be an effective oral outpatient treatment option for ESBL-EC. In vitro synergistic testing is simple and predictive of successful treatment.

Characterization of the First OXA-10 Natural Variant with Increased Carbapenemase Activity

While carbapenem resistance in Gram-negative bacteria is mainly due to the production of efficient carbapenemases, β-lactamases with a narrower spectrum may also contribute to resistance when combined with additional mechanisms. OXA-10-type class D β-lactamases, previously shown to be weak carbapenemases, could represent such a case. In this study, two novel OXA-10 variants were identified as the sole carbapenem-hydrolyzing enzymes in meropenem-resistant enterobacteria isolated from hospital wastewater and found by next-generation sequencing to express additional β-lactam resistance mechanisms. The new variants, OXA-655 and OXA-656, were carried by two related IncQ1 broad-host-range plasmids. Compared to the sequence of OXA-10, they both harbored a Thr26Met substitution, with OXA-655 also bearing a leucine instead of a valine in position 117 of the SAV catalytic motif. Susceptibility profiling of laboratory strains replicating the natural bla _OXA plasmids and of recombinant clones expressing OXA-10 and the novel variants in an isogenic background indicated that OXA-655 is a more efficient carbapenemase. The carbapenemase activity of OXA-655 is due to the Val117Leu substitution, as shown by steady-state kinetic experiments, where the k _cat of meropenem hydrolysis was increased 4-fold. In contrast, OXA-655 had no activity toward oxyimino-β-lactams, while its catalytic efficiency against oxacillin was significantly reduced. Moreover, the Val117Leu variant was more efficient against temocillin and cefoxitin. Molecular dynamics indicated that Val117Leu affects the position 117-Leu155 interaction, leading to structural shifts in the active site that may alter carbapenem alignment. The evolutionary potential of OXA-10 enzymes toward carbapenem hydrolysis combined with their spread by promiscuous plasmids indicates that they may pose a future clinical threat.

Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings

The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.

Rapid in vitro detection of CTX-M groups 1, 2, 8, 9 resistance genes by LAMP assays

BACKGROUND

The prevalence of bacteria producing CTX-M Extended-Spectrum β-lactamases (ESBLs) has increased around the world and some of them became a major cause of infections such as bloodstream or urinary tract infections (UTI). We developed a loop-mediated isothermal amplification (LAMP) assay for a simple, rapid and sensitive detection of the four most common CTX-M groups, namely CTX-M groups 1, 2, 8 and 9.

METHODS

LAMP primers targeting the four ESBLs CTX-M groups were designed using the Primer Explorer V4 software. The detection limit of the method was tested by serial dilution of reference DNAs. The primer specificity of the LAMP reaction was tested on DNA extracted from six strains producing various group of CTX-M and validated using DNA extracted from CTX-M-resistant clinical isolates (isolated from pus, urine, or blood). Results were compared with those of conventional PCR.

RESULTS

We were able to detect down to 0.1 pg/ul of DNA using the newly developed LAMP assays whereas the minimal amount detectable for conventional PCR was 50 to 100pg/ul, indicating that the LAMP assay was found to have a detection limit at least 500 to 1000 times lower than the PCR. Additionally, representative genes from the CTX-M groups 1, 2, 8 and 9 were amplified using the designed assay and no cross amplification was observed between the four CTX-M groups, demonstrating the specificity of the LAMP assay. Of the 37 clinical strains tested, the four LAMP assays showed 100% sensitivity and 87%, 97%, 100%, 100% specificity for the CTX-M groups 1, 2, 8 and 9 respectively.

CONCLUSION

Being sensitive, specific, rapid and standard methods, the LAMP assays developed in this study have a potential to be beneficial tools in molecular epidemiology and surveillance studies of the four prevalent EBSLs CTX-M groups even in low cost laboratory.

Incidence and molecular characterization of the extended spectrum beta lactamase-producing Escherichia coli isolated from urinary tract infections in Eastern Saudi Arabia

Objectives:

To find the prevalence of uropathogenic Escherichia coli (E. coli)-producing extended spectrum beta lactamase (ESBL) at King Fahd Military Medical Complex in Dhahran (KFMMC) and to detect the genes responsible for its production. In addition, we determined the pattern of multi-drug resistance among isolates.

Methods:

A total of 117 uropathogenic E. coli isolates were collected from KFMMC over a period of 4 months from March 2014 to June 2014. These were received in the Microbiology Laboratory at Prince Sultan Military College of Health Sciences (PSMCHS), Dhahran, Saudi Arabia for analysis. The isolates were screened for ESBL using VITEK^® 2 Compact. Polymerase chain reaction (PCR) examination was used to determine TEM, SHV, and CTX-M genes.

Results:

Our findings indicated that there is a high incidence of ESBLs among the E. coli isolated from UTI (23.1%). Our study also indicated that CTX-M genes are the most prevalent among the isolates at KFMMC followed by TEM class (6%), but there was also a higher percentage E. coli (3.4%) simultaneously harboring TEM and CTX-M genes. None of our isolates harbored the SHV genes.

Conclusion:

The findings document the threat of ESBL among E. coli isolates from UTI especially the CTX-M class in our hospital with the occurrence of these strains as etiologic agents of infection in the hospital and community.

Genomic Identity of Fluoroquinolone-Resistant blaCTX-M-15-Type ESBL and pMAmpC β-Lactamase Producing Klebsiella pneumoniae from Buffalo Milk, India

We investigated the occurrence of extended-spectrum β-lactamase (ESBL) and AmpC-type β-lactamase (ACBL) producing quinolone-resistant Klebsiella pneumoniae (KP) in milk samples of apparently healthy buffaloes (n = 348) and buffaloes (n = 19) with evidence of subclinical mastitis from seven districts of West Bengal, India. In total, 12 ESBL producing KP were isolated with blaCTX-M-15 gene and 7 of them were ACBL producers, as well. The blaCTX-M-15 genes were carried by transposable element ISEcp1. The plasmid-mediated quinolone resistance genes-qnrS, qnrA, qnrB, qepA, and aac(6')-Ib-cr were detected in five, one, three, four, and one isolate (s), respectively. In addition, eight isolates carried mutation in gyrase (gyrA) and six in topoisomerase IV (parC). Resistance markers/genes for sulfonamide (sul1), tetracycline [tet(A) and tet(B)], and aminoglycoside (aacC2) were also detected in eight, four, and one isolate(s), respectively. The class I integrons identified in five isolates carried aad2/aad5 and dfrA12/dfrA17 gene cassettes. The enterobacterial repetitive intergenic consensus-PCR revealed that all the isolates were genetically diverse and comprised a heterogeneous population. Isolation of multidrug-resistant KP, a typical nosocomial pathogen from buffalo milk, reiterates the need to monitor farm animals for ESBL producing Enterobacteriaceae and emphasizes on judicious use of antibiotics in animal husbandry sector.

The Molecular and Clinical Epidemiology of Extended-Spectrum Cephalosporin- and Carbapenem-Resistant Enterobacteriaceae at 4 US Pediatric Hospitals

OBJECTIVE

In this report, we aim to describe the epidemiology of extended-spectrum cephalosporin-resistant (ESC-R) and carbapenem-resistant (CR) Enterobacteriaceae infections in children.

METHODS

ESC-R and CR Enterobacteriaceae isolates from normally sterile sites of patients aged <22 years from 4 freestanding pediatric medical centers were collected along with the associated clinical data.

RESULTS

The overall frequencies of ESC-R and CR isolates according to hospital over the 4-year study period ranged from 0.7% to 2.8%. Rates of ESC-R or CR Escherichia coli and Klebsiella pneumoniae varied according to hospital and ranged from 0.75 to 3.41 resistant isolates per 100 isolates (P < .001 for any differences). E coli accounted for 272 (77%) of the resistant isolates; however, a higher rate of resistance was observed in K pneumoniae isolates (1.78 vs 1.27 resistant isolates per 100 same-species isolates, respectively; P = .005). One-third of the infections caused by ESC-R or CR E coli were community-associated. In contrast, infections caused by ESC-R or CR K pneumoniae were more likely than those caused by resistant E coli to be healthcare- or hospital-associated and to occur in patients with an indwelling device (P ≤ .003 for any differences, multivariable logistic regression). Nonsusceptibility to 3 common non-β-lactam agents (ciprofloxacin, gentamicin, and trimethoprim-sulfamethoxazole) occurred in 23% of the ESC-R isolates. The sequence type 131-associated fumC/fimH-type 40-30 was the most prevalent sequence type among all resistant E coli isolates (30%), and the clonal group 258-associated allele tonB79 was the most prevalent allele among all resistant K pneumoniae isolates (10%).

CONCLUSIONS

The epidemiology of ESC-R and CR Enterobacteriaceae varied according to hospital and species (E coli vs K pneumoniae). Both community and hospital settings should be considered in future research addressing pediatric ESC-R Enterobacteriaceae infection.