Variations in the prevalence of strains expressing an extended-spectrum beta-lactamase phenotype and characterization of isolates from Europe, the Americas, and the Western Pacific region

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

BACKGROUND

In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age.

RESULTS

We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs.

CONCLUSIONS

We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

Epidemiology and risk factors for recurrence in biliary source bloodstream infection episodes in oncological patients

We aimed to describe the characteristics and outcomes of biliary source bloodstream infections (BSIs) in oncological patients. Secondarily, we analyzed risk factors for recurrent BSI episodes. All episodes of biliary source BSIs in oncological patients were prospectively collected (2008-2019) and retrospectively analyzed. Logistic regression analyses were performed. A rule to stratify patients into risk groups for recurrent biliary source BSI was conducted. Four hundred biliary source BSIs were documented in 291 oncological patients. The most frequent causative agents were Escherichia coli (42%) and Klebsiella spp. (27%), and 86 (21.5%) episodes were caused by multidrug-resistant Gram-negative bacilli (MDR-GNB). The rates of MDR-GNB increased over time. Overall, 73 patients developed 118 recurrent BSI episodes. Independent risk factors for recurrent BSI episodes were prior antibiotic therapy (OR 3.781, 95% CI 1.906-7.503), biliary prosthesis (OR 2.232, 95% CI 1.157-4.305), prior admission due to suspected biliary source infection (OR 4.409, 95% CI 2.338-8.311), and BSI episode caused by an MDR-GNB (OR 2.857, 95% CI 1.389-5.874). With these variables, a score was generated that predicted recurrent biliary source BSI with an area under the receiver operating characteristic (ROC) curve of 0.819. Inappropriate empirical antibiotic treatment (IEAT) was administered in 23.8% of patients, and 30-d mortality was 19.5%. As a conclusion, biliary source BSI in oncological patients is mainly caused by GNB, with high and increasing MDR rates, frequent IEAT, and high mortality. Recurrent BSI episodes are frequent. A simple score to identify recurrent episodes was developed to potentially establish prophylactic strategies. IMPORTANCE This study shows that biliary source bloodstream infections (BSIs) in oncological patients are mainly caused by Gram-negative bacilli (GNB), with high and increasing rates of multidrug resistance. Importantly, recurrent biliary source BSI episodes were very frequent and associated with delays in chemotherapy, high rates of inappropriate empirical antibiotic therapy, and high 30-d mortality (19.5%). Using the variable independently associated with recurrent BSI episodes, a score was generated that predicted recurrent biliary source BSI with high accuracy. This score could be used to establish prophylactic strategies and lower the risk of relapsing episodes and the associated morbidity and mortality.

ESBL in positive hemoculture of a Southern-Brazil Teaching Hospital's Intensive Care Units

Bloodstream infections are among the most serious and frequent infections, and the people most exposed are patients in the Intensive Care Unit (ICU). ESBL (extended-spectrum beta-lactate) are resistant bacteria to penicillins, cephalosporins and monobactams. It´s necessary to know how often and which microorganisms are involved, checking their susceptibility. This study was carried out at the University Hospital. Data collection was performed in the Adult and Newborn ICUs, with assessment of microorganisms and their resistance profile. During six-month period, 156 samples were studied, and 42 were positive with microorganism isolation. Isolated species include Staphylococcus aureus, Staphylococcus epidermidis and Klebsiella pneumoniae. Many resistant to carbapenem.

Monitoring fluoroquinolone resistance among ESBL-positive and ESBL-negative Escherichia coli strains isolated from urinary tract infections: An alert for empirical treatment

BACKGROUND

Bacterial resistance to extended-spectrum beta-lactamases (ESBL) is present worldwide. Empirical antibiotic therapy is often needed, and the use of fluoroquinolones, such as ciprofloxacin and norfloxacin, is common. This study aimed to analyze the urine cultures from 2,680 outpatients in January 2019, 2020, 2021, and 2022, with bacterial counts above 100,000 CFU/mL in which Escherichia coli was the etiological agent.

METHODS

We monitored the resistance of ESBL-positive and ESBL-negative strains to ciprofloxacin and norfloxacin and evaluated resistance rates.

RESULTS

Significantly higher fluoroquinolone resistance rates were observed among ESBL-positive strains in all years studied. Furthermore, a significant increase in the rate of fluoroquinolone resistance was observed between 2021 and 2022 in ESBL-positive and -negative strains, as well as from 2020 to 2021 among the ESBL-positive strains.

CONCLUSIONS

The data obtained in the present study showed a tendency towards an increase in fluoroquinolone resistance among ESBL-positive and -negative E. coli strains isolated from urine cultures in Brazil. Since empirical antibiotic therapy with fluoroquinolones is commonly used to treat diverse types of infections, such as community-acquired urinary tract infections, this work highlights the need for continuous monitoring of fluoroquinolone resistance among E. coli strains circulating in the community, which can mitigate the frequency of therapeutic failures and development of widespread multidrug-resistant strains.

Molecular Characterization of Extensively Drug Resistant Salmonella Enterica Serovar Typhi Clinical Isolates from Lahore, Pakistan

Background

The emergence of extensively drug-resistant (XDR) typhoid in Pakistan has endangered the treatment options available to manage this infection. Third generation cephalosporin were the empiric choice to treat typhoid fever in Pakistan, but acquisition of ESBLs have knocked them out of the arsenal. The current empiric choice is azithromycin which is vulnerable to resistance too. This study aimed to assess the burden of XDR typhoid and the frequency of resistance determinants in blood culture samples collected from different hospitals in Lahore, Pakistan.

Methods

A total of 835 blood cultures were collected from different tertiary care hospitals in Lahore during January 2019 to December 2021. Among 835 blood cultures, 389 Salmonella Typhi were identified, and 150 were XDR S. Typhi (resistant to all recommended antibiotics). Antibiotics resistance genes of the first-line drugs (bla_TEM-1, catA1, sul1, and dhfR7) and second line drugs (gyrB, gyrA, qnrS, ParC and ParE) were investigated among XDR S. Typhi. There were different CTX-M genes isolated using the specific primers, bla_CTX-M-U, bla_CTX-M-1, bla_CTX-M-15, bla_CTX-M-2, bla_CTX-M-8 and bla_CTX-M-9.

Results

Antibiotic resistant genes of the first-line drugs were isolated with different frequency, bla_TEM-1 (72.6%), catA1 (86.6%), sul1 (70%), and dhfR7 (56%). Antibiotics resistance genes of second-line drugs were isolated as: gyrB (60%), gyrA (49.3%), qnrS (32.6%), parC (44%) and parE (28%). Among CTX-M genes, bla_CTX-M-U (63.3%) was the most frequent followed by bla_CTX-M-15 (39.3%) and bla_CTX-M-1 (26%).

Conclusion

Our study concluded that XDR isolates circulating in Pakistan have acquired first-line and second-line antibiotic resistant genes quite successfully along with CTX-M genes (ESBLs) rendering them resistant to the third generation cephalosporins as well. Emergence of azithromycin resistance in XDR S. Typhi which is currently used as an empiric treatment option is worrisome and needs to be monitored carefully in endemic countries like Pakistan.

Multidrug-Resistant Enterobacterales in Community-Acquired Urinary Tract Infections in Djibouti, Republic of Djibouti

The emergence and spread of multidrug resistant Enterobacterales (MDR-E) are a global public health issue. This problem also concerns urinary tract infections (UTI), which are the second most frequent infections after respiratory infections. The objective of this study was to determine MDR-E frequency and to characterize MDR-E isolates from patients with community-acquired UTIs in Djibouti, Republic of Djibouti. From 800 clinical urinary samples collected at the Mer Rouge Laboratory, Djibouti, from January to July 2019, 142 were identified as Enterobacterales (age range of the 142 patients mean age is 42 years.) Mass spectrometry analysis of these isolates identified 117 Escherichia coli, 14 Klebsiella pneumoniae, 2 Proteus mirabilis, 4 Enterobacter spp., 4 Providencia stuartii and 1 Franconibacter helveticus. Antibiotic susceptibility testing (disk diffusion method) of these 142 isolates detected 68 MDR-E (68/142 = 48%): 65 extended-spectrum bêta lactamase- (ESBL), 2 carbapenemase- (one also ESBL), and 1 cephalosporinase-producer. Multiplex PCR and sequencing showed that the 65 ESBL-producing isolates carried genes encoding CTX-M enzymes (CTX-M-15 in 97% and CTX-M-9 in 3% of isolates). Two isolates harboured a gene encoding the OXA-48-like carbapenemase, and one the gene encoding the AmpC CMY-2 cephalosporinase. Genes implicated in resistance to quinolones (qnrB, aac (6')-Ib-cr, qnrD, oqxA and B) also were detected. Among the E. coli phylogroups, B2 was the most common phylogenetic group (21% of MDR-E isolates and 26% of non-MDR-E isolates), followed by A (14% and 12%), B1 (9% and 7%), D (3% and 3%), F (3% and 3%) and E (2% and 2%). This study highlights the high frequency of ESBL producers and the emergence of carbapenemase-producers among Enterobacterales causing community-acquired UTIs in Djibouti.

Risk factors and outcome due to extended-spectrum β-lactamase-producing uropathogenic Escherichia coli in community-onset bloodstream infections: A ten-year cohort study in Sweden

Objective

To study clinical outcome and risk factors associated with extended-spectrum β-lactamase (ESBL)-producing uropathogenic Escherichia coli (UPEC) in community-onset bloodstream infections (CO-BSI).

Methods

This was a population-based cohort study including patients with pheno- and genotype-matched ESBL-producing E. coli and non-ESBL- E. coli in urine and blood samples collected in 2009–2018 in southeast Sweden. Seventy-seven episodes of ESBL-UPEC satisfying the inclusion criteria were matched 1:1 with 77 non-ESBL-UPEC for age, gender, and year of culture.

Results

The most common ST-type and ESBL gene was ST131 (55%), and bla_CTX-M-15 (47%), respectively. Risk factors for ESBL-UPEC were: previous genitourinary invasive procedure (RR 4.66; p = 0.005) or history of ESBL-producing E. coli (RR 12.14; p = 0.024). There was significant difference between ESBL-UPEC and non-ESBL-UPEC regarding time to microbiologically appropriate antibiotic therapy (27:15 h vs. 02:14 h; p = <0.001) and hospital days (9 vs. 5; p = <0.001), but no difference in 30-day mortality (3% vs. 3%; p = >0.999) or sepsis within 36 hours (51% vs. 62%; p = 0.623) was observed.

Conclusion

The predominant risk factors for ESBL-UPEC were history of ESBL-Ec infection and history of genitourinary invasive procedure. The overall mortality was low and the delay in appropriate antibiotic therapy did not increase the risk for 30-day mortality or risk for sepsis within 36 hours among patients infected with ESBL UPEC. However, these results must be regarded with some degree of caution due to the small sample size.

Comparison of approaches for source attribution of ESBL-producing Escherichia coli in Germany

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.

Phenotypic and Molecular Characterization of CTX-M Type B-Lactamases in Gram Negative Bacterial Strains Isolated from Hospitals, Lahore, Pakistan

One of the principal mechanisms that contribute resistance to antibiotics is the production of extended spectrum beta lactamase (ESBL) in Gram negative bacteria. In the present study, molecular methods were used to evaluate the prevalence of the extended-spectrum beta-lactamase (ESBL)-encoding CTX-M gene among Gram negative bacterial strains. In total, 148 clinical samples were collected from different tertiary care hospitals of Lahore, Pakistan. Disc synergy diffusion method was used to detect the presence of ESBL production. Moreover, antibiotic resistance patterns and molecular detection of bla _CTX-M ESBLs, were also studied. The pathogens isolated from the 148 samples included Escherichia coli (43%) followed by Klebsiella sp. (28%), Proteus sp. (18%) and Pseudomonas sp. (11%). In all 148 strains, 95 (64%) were ESBL producers while 53 (36%) were non ESBL producers. The strains which were phenotypically ESBL producers, bla _CTX-M were found in 46% E. coli strains, while 50% Klebsiella sp. were harboring the gene. A high resistance rate was observed against cephalosporins (cefopodoxime 67%, cefoperazone 73%, cephalexin 63% sparaxin 61%). Lower resistance was observed against meropenem among all isolated bacterial strains. Genotypic detection of bla _CTX-M genes by PCR revealed 46% of E. coli and 50% of Klebsiella strains harbored bla _CTX-M gene. The present study showed that ESBLs producers were resistant to commonly used antibiotics. Similarly, bla _CTX-M ESBL production is more prevalent in our clinical isolates.

High Prevalence of Antimicrobial Resistance and Integron Gene Cassettes in Multi-Drug-Resistant Klebsiella pneumoniae Isolates From Captive Giant Pandas (Ailuropoda melanoleuca)

Multi-drug-resistant Klebsiella pneumoniae (MDR K. pneumonia) is increasingly being reported with corresponding increase in morbidity and mortality all over the world. However, limited information is available concerning MDR K. pneumonia in giant pandas. The objective of this study was to grasp the drug resistance profile of MDR K. pneumonia isolated from giant pandas. A total of 182 K. pneumoniae isolates were collected from fresh feces of 94 captive giant pandas of different ages and sex and separated by season. We performed a standard disk diffusion antimicrobial susceptibility test with the isolates and further evaluated the antibiotic resistance genes (ARGs) of multi-drug-resistant strains by high-throughput quantitative PCR. In addition, we then analyzed mobile genetic elements (MGEs), integron gene cassettes, and the multi-locus sequence typing of multi-drug-resistant strains by PCR. Antimicrobial susceptibility testing results demonstrated that a total of 30 (16.5%) K. pneumoniae isolates showed multiple drug resistances. The thirty MDR K. pneumonia isolates were mainly resistant to amoxicillin (100.0%), doxycycline (86.7%), chloramphenicol (60.0%), compound trimethoprim (60.0%) and trimethoprim (56.7%). Fifty different types of antibiotic resistance genes were found, which included a total of 671 antibiotic resistance genes, in the 30 multi-drug-resistant isolates. The top ten resistance genes were: vanTC-02, aacC, blaCTX-M-04, blaSHV-01, blaSHV-02, ampC-04, blaOXY, tetD, blaTEM and tetA-02. Thirteen mobile genetic elements were detected, of which IS26 (96.67%) and intI1 (96.67%) had the highest frequency. The thirty MDR K. pneumonia isolates were negative for the traA, traF, tnsA, IS1133, ISpa7, ISkpn6, intI2 and intI3 genes. Moreover, a further investigation of integrons revealed that two types of specific gene cassettes (dfrA12 + orfF + aadA2 and dfrA12 + orfF) were identified in class 1 integrons. Multi-locus sequence typing results showed that 22 STs in the thirty MDR K. pneumonia isolates were identified, the main type was ST37 (5/30). Our results illustrate that effective surveillance and strict biosecurity strategies should be taken to prevent the spread of multi-drug-resistant bacteria, and monitor the emergence of mobile genetic elements and integrons.

Spatial, Ecologic, and Clinical Epidemiology of Community-Onset, Ceftriaxone-Resistant Enterobacteriaceae, Cook County, Illinois, USA

We performed a spatial and mixed ecologic study of community-onset Enterobacteriaceae isolates collected from a public healthcare system in Cook County, Illinois, USA. Individual-level data were collected from the electronic medical record and census tract–level data from the US Census Bureau. Associations between individual- and population-level characteristics and presence of ceftriaxone resistance were determined by logistic regression analysis. Spatial analysis confirmed nonrandom distribution of ceftriaxone resistance across census tracts, which was associated with higher percentages of Hispanic, foreign-born, and uninsured residents. Individual-level analysis showed that ceftriaxone resistance was associated with male sex, an age range of 35–85 years, race or ethnicity other than non-Hispanic Black, inpatient encounter, and percentage of foreign-born residents in the census tract of isolate provenance. Our findings suggest that the likelihood of community-onset ceftriaxone resistance in Enterobacteriaceae is influenced by geographic and population-level variables. The development of effective mitigation strategies might depend on better accounting for these factors.

Detection of Quorum Sensing N-Acyl-Homoserine Lactone Molecules Produced by Different Resistant Klebsiella pneumoniae Isolates Recovered from Poultry and Different Environmental Niches

This study aimed to detect and identify the N-acyl-homoserine lactones molecules (AHLs) produced by different resistant Klebsiella pneumoniae isolates recovered from poultry and environmental samples using a modified validated high-performance liquid chromatography method. A total of 56 K. pneumoniae isolates were recovered, investigated for their antibiotic susceptibility, and screened for AHLs production using the Agrobacterium tumefaciens NTL4 biosensor system and a validated high-performance liquid chromatography method. The results revealed the detection of different short- and long-chain AHLs molecules among 39 K. pneumoniae isolates recovered from poultry and environmental samples. All environmental isolates produced nine peaks with retention times for C4-HSL, C6-HSL, C12-HSL, C8-HSL, C14-HSL, C8-oxo-HSL, C10-HSL, C6-oxo-HSL, and C7-HSL. The most quantifiable AHL signal molecules in poultry isolates were C4-HSL, C6-HSL, and C12-HSL. No statistical correlation between the AHL-producing ability of K. pneumoniae isolates and antibiotic resistance was reported. To the best of our knowledge, this study provides the first detailed report on the detection and identification of AHLs in K. pneumoniae isolates recovered from poultry and environmental samples. Furthermore, it provides a new insight available tool other than LC-MS/MS for detection and identification of AHL molecules.

Real-Time Single-Cell Imaging Reveals Accelerating Lipid Peroxyl Radical Formation in Escherichia coli Triggered by a Fluoroquinolone Antibiotic

The formation of reactive oxygen species (ROS) induced by bactericidal antibiotics has been associated with a common, nonspecific mechanism of cellular death. Herein, we report real-time single-cell fluorescence studies on Escherichia coli stained with a fluorogenic probe for lipid peroxyl radicals showing the generation of this form of ROS when exposed to the minimum inhibitory concentration (MIC) and 10× MIC of the fluoroquinolone antibiotic ciprofloxacin (3 and 30 μM, respectively). Single-cell intensity-time trajectories show an induction period followed by an accelerating phase for cells treated with antibiotic, where initial and maximum intensity achieved following 3.5 h of incubation with antibiotic showed dose-dependent average values. A large fraction of bacteria remains viable after the studies, indicating ROS formation is occurring a priori of cell death. Punctate structures are observed, consistent with membrane blebbing. The addition of a membrane embedding lipid peroxyl radical scavenger, an α-tocopherol analogue, to the media increased the MIC of ciprofloxacin. Lipid peroxyl radical formation precedes E. coli cell death and may be invoked in a cascade event including membrane disruption and consequent cell wall permeabilization. Altogether, our work illustrates that lipid peroxidation is caused by ciprofloxacin in E. coli and suppressed by α-tocopherol analogues. Lipid peroxidation may be invoked in a cascade event including membrane disruption and consequent cell wall permeabilization. Our work provides a methodology to assess antibiotic-induced membrane peroxidation at the single-cell level; this methodology provides opportunities to explore the scope and nature of lipid peroxidation in antibiotic-induced cell lethality.

Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance

Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how antibiotics affect within-host resistance dynamics. Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We use blaCTX-M (the most widespread ESBL gene family) and 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal swabs from 133 ESBL-positive patients followed up in a prospective cohort study in three European hospitals. We find that cefuroxime and ceftriaxone are associated with increased blaCTX-M abundance during treatment (21% and 10% daily increase, respectively), while treatment with meropenem, piperacillin-tazobactam, and oral ciprofloxacin is associated with decreased blaCTX-M (8% daily decrease for all). The model predicts that typical antibiotic exposures can have substantial long-term effects on blaCTX-M carriage duration.

Multidrug-resistant Escherichia coli isolated from a dog with a history of urolithiasis: case report

ABSTRACT Bacterial resistance is a reality in both human and veterinary health, it limits the therapeutic arsenal and raises the costs of the patient’s treatment. A dog with signs of cystitis received treatment with 5mg/kg enrofloxacin at three consecutive times, with low effectiveness. The presence of urethral uroliths was identified and urohydropulsion was done. The animal presented a new obstruction, for which a cystotomy was performed, but continued with signs of infection. Uroculture and antimicrobial susceptibility test were then performed. Escherichia coli was identified, which was resistant to 13 antibiotics, being sensitive only to piperacillin-tazobactam and amikacin. In the screening test for β-lactamase, the production of ESβL was detected. The qPCR indicated the presence of the bla CTXm, bla DHA, bla OXA, bla IMP, bla TEM, bla GIM, bla SIM, bla SPM and bla SME genes, which may lead to a phenotypic resistance profile for ampicillin, amoxicillin-clavulanate, aztreonam, cefepime cefoxitin, cefuroxime, ceftazidime, ceftriaxone, imipenem, and piperacillin-tazobactam. This case reaffirms the value that laboratory analysis adds to the diagnosis and treatment of cystitis and urolithiasis, which can define the direction of evolution of the prognosis and the speed at which the patient's health will be restored.

Detection and genetic characterization of extended-spectrum beta-lactamases producers in a tertiary care hospital

BACKGROUND

Extended-spectrum beta-lactamase (ESBL)-producing organisms inactivate extended beta-lactam antibiotics and monobactams and also exhibit coresistance to many other classes of antibiotics. The present study was carried out to assess the prevalence of the ESBLs and to determine the most prevalent genotype in our hospital.

MATERIALS AND METHODS

All clinically significant Gram-negative isolates were identified, and their antimicrobial susceptibility testing was done by Kirby-Bauers' disc diffusion method. ESBL detection was confirmed by minimal inhibitory concentration method using agar dilution technique for those who screened positive by ceftazidime (30 μg) disc. Further, the established ESBL-positive isolates were subjected to genotyping for bla TEM, bla CTX-M, and bla SHV genes by using conventional polymerase chain reaction.

RESULTS

Escherichia coli was the most common (28.84%) Gram-negative bacillus followed by Klebsiella pneumoniae (18.07%), while Pseudomonas spp. (9.61%) was the most commonly identified nonfermenter. ESBL production was detected in 160 (30.8%) isolates. Klebsiella oxytoca (46.7%) followed by E. coli (44%) were the common ESBL producers. Most predominant ESBL gene was bla TEM, found in 122 (76.25%) isolates. Combinations of two genes were seen in 109 (68.1%) isolates, the most common (43.12%) combination being bla_TEM and bla_CTX-M. In this study, 16 (10%) strains had all the three types of genes. Most of the isolated Gram-negative bacilli (GNB) were sensitive to amikacin, imipenem, and colistin.

CONCLUSION

In our study, the 30.8% of GNB were ESBL producers. This is the only study that shows that TEM is the most prevalent ESBL genotypes in our area. Of concern is a good number of isolates showing all three patterns of genes (TEM, SHV, and CTX-M). Amikacin, imipenem, and colistin were the most useful antibiotics in our setup.

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.

Shigella flexneri: an emerging pathogen

Shigella flexneri is a leading etiologic agent of diarrhea in low socioeconomic countries. Notably, various serotypes in S. flexneri are reported from different regions of the world. The precise approximations of illness and death owing to shigellosis are missing in low socioeconomic countries, although it is widespread in different regions. The inadequate statistics available reveal S. flexneri to be a significant food and waterborne pathogen. All over the world, different antibiotic-resistant strains of S. flexneri serotypes have been emerged especially multidrug-resistant strains. Recently, increased resistance was observed in cephalosporins (3rd generation), azithromycin, and fluoroquinolones. There is a need for a continuous surveillance study on antibiotic resistance that will be helpful in the update of the antibiogram. The shigellosis burden can be reduced by adopting preventive measures like delivery of safe drinking water, suitable sanitation, and development of an effective and inexpensive multivalent vaccine. This review attempts to provide the recent findings of S. flexneri related to epidemiology and the emergence of multidrug resistance.

Clinical epidemiology and outcomes of biliary tract infections caused by Klebsiella pneumoniae

Background

Biliary tract infection (BTI) is a common cause of bacteremia, and is associated with high morbidity and mortality. The clinical epidemiology and outcomes of BTI caused by Klebsiella pneumoniae (KP) have not been well investigated.

Methods

This was a retrospective study performed at a university teaching hospital in China from May 2012 to June 2017 that analyzed data for 119 patients with BTI caused by KP. We identified KP from bile cultures obtained before endoscopic or surgical treatment. Patients' demographic characteristics and clinical outcomes were also recorded.

Results

Forty-seven KP strains (39.5%) were positive for the extended spectrum beta-lactamase (ESBL) phenotype. The ESBL-positive group had a higher rate of stay in ICU [12.8% vs. 1.4% (ESBL-negative group); P=0.015] and a significantly longer hospital stay (30.79±31.512 vs. 20.06±23.945 days, respectively; P=0.037). There were no significant differences for 30-day mortality between the two groups; 112 (94.1%) patients survived and 7 (5.9%) died within 30-days of onset. Univariate analysis showed that nonsurvivors were significantly more likely to be older (66.46±22.34 vs. 46±14.84 years, respectively; P=0.001), and have hypoproteinemia (5/7, 71.4% vs. 21/112, 18.8%; P=0.006), immunosuppression (3/7, 42.9% vs. 4/112, 3.6%; P=0.004), solid tumors (5/7, 71.4% vs. 20/112, 17.9%; P=0.004), bloodstream infections (6/7, 85.7% vs. 22/112, 19.6%; P=0.001), and lower surgery rates (1/7, 14.3% vs. 66/112, 58.9%; P=0.042) compared with survivors, respectively. However, we found no significant independent risk factor for mortality. The malignant biliary obstruction group was significantly more likely to have chronic liver disease (P=0.035) than the benign biliary obstruction group, and mortality was higher for the malignant biliary obstruction group (5/25, 20% vs. 2/94, 2.1%, respectively; P=0.05). The malignant biliary group also had higher alkaline phosphatase, and direct and total bilirubin direct levels. Multivariate analysis showed that chronic liver disease was an independent risk factor in patients with malignant biliary disease [odds ratio (OR), 2.431; 95% confidence interval, 1.834-4.031; P=0.001].

Conclusions

Patients with BTI caused by KP were more likely to have the ESBL phenotype, and antibiotic resistance was not associated with overall survival. Patients with malignant biliary obstruction had higher mortality, and chronic liver disease was an independent risk factor.

Multidrug resistance and risk factors associated with community-acquired urinary tract infections caused by Escherichia coli in Venezuela

INTRODUCTION

The treatment of urinary tract infections has become more challenging due to the increasing frequency of multidrug-resistant Escherichia coli in human populations.

OBJECTIVE

To characterize multidrug-resistant E. coli isolates causing community-acquired urinary tract infections in Cumaná, Venezuela, and associate possible risk factors for infection by extended-spectrum beta-lactamases (ESBL)-producing isolates.

MATERIALS AND METHODS

We included all the patients with urinary tract infections attending the urology outpatient consultation and emergency unit in the Hospital de Cumaná, Estado Sucre, Venezuela, from January through June, 2014. blaTEM, blaSHV and blaCTX-M genes detection was carried out by PCR.

RESULTS

We found a high prevalence of multidrug-resistant E. coli (25.2%) with 20.4% of the isolates producing ESBL. The ESBL-producing isolates showed a high frequency (66.7%) of simultaneous resistance to trimethoprim-sulphamethoxazole, fluoroquinolones and aminoglycosides compared to non-producing isolates (2.4%). Of the resistant isolates, 65.4% carried the blaTEM gene, 34.6% the blaCTX-M and 23.1% the blaSHV. The blaCTX-M genes detected belonged to the CTX-M-1 and CTX-M-2 groups. Plasmid transfer was demonstrated by in vitro conjugation in 17 of the 26 ESBL-producing isolates. All three genes detected were transferred to the transconjugants. Age over 60 years, complicated urinary tract infections and previous use of a catheter predisposed patients to infection by ESBL-producing E. coli.

CONCLUSIONS

The high frequency of multidrug-resistant ESBL-producing isolates should alert the regional health authorities to take measures to reduce the risk of outbreaks caused by these types of bacteria in the community.

Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States

Background

Sequencing technologies and techniques have seen remarkable transformation and innovation that have significantly affected sequencing capability. Data analyses have replaced sequencing as the main challenge. This paper provides an overview on applying next-generation sequencing (NGS) and analysis and discusses the benefits and challenges. In addition, this document shows results from using NGS and bioinformatics tools to screen for β-lactamase genes and assess the epidemiological structure of Escherichia coli– and Klebsiella pneumoniae–causing bloodstream (BSIs) and urinary tract (UTIs) infections in patients hospitalized in the United States during the SENTRY Antimicrobial Surveillance Program for 2016.

Methods

A total of 3525 isolates (2751 E. coli and 774 K. pneumoniae) causing BSIs (n = 892) and UTIs (n = 2633) in hospitalized patients in the United States were included. Isolates were tested for susceptibility by broth microdilution, and those that met a minimum inhibitory concentration (MIC)–based screening criteria had their genomes sequenced and analyzed.

Results

A total of 11.6% and 16.1% of E. coli–causing UTIs and BSIs, respectively, met the MIC-based criteria, whereas 11.0% and 13.7% of K. pneumoniae isolates causing UTIs and BSIs, respectively, met the criteria. Among E. coli, bla_CTX-M variants (87.6% overall) prevailed (60.5% of CTX-M group 1 and 26.9% of group 9). A total of 60.3% of K. pneumoniae isolates carried bla_CTX-M variants (52.7% and 7.6% of groups 1 and 9, respectively). Two E. coli (0.6%) and 13 K. pneumoniae (12.9%) isolates harbored bla_KPC. Among KPC-producing K. pneumoniae (2 from BSIs and 11 from UTIs), 84.6% (11/13) were ST258 (CC258). Seventeen and 38 unique clonal complexes (CCs) were noted in E. coli that caused BSIs and UTIs, respectively, and CC131 (or ST131) was the most common CC among BSI (53.6%) and UTI (58.2%) isolates. Twenty-three and 26 CCs were noted among K. pneumoniae–causing BSIs and UTIs, respectively. CC258 (28.3%) prevailed in UTI pathogens, whereas CC307 (15.0%) was the most common CC among BSI isolates.

Conclusions

This study provides a benchmark for the distribution of β-lactamase genes and the population structure information for the most common Enterobacteriaceae species responsible for BSIs and UTIs in US medical centers during the 2016 SENTRY Program.

Local prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae intestinal carriers at admission and co-expression of ESBL and OXA-48 carbapenemase in Klebsiella pneumoniae: a prevalence survey in a Spanish University Hospital

OBJECTIVE

To assess the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) faecal carriers at admission in a University Hospital in Spain.

DESIGN

Prevalence survey.

SETTING

Pneumology, gastroenterology, urology and neurosurgery units at a university tertiary hospital in Madrid (Spain).

PARTICIPANTS

A total of 10 643 patients aged 18 and older admitted from March 2014 to April 2016 with a rectal swab taken at admission or as soon as possible within the first 48 hours.

PRIMARY AND SECONDARY OUTCOME MEASURES

Prevalence of ESBL-E faecal carriers and prevalence of ESBL-E infections at admission.

RESULTS

The prevalance of ESBL-E carriers at admission was 7.69% (CI 95% 7.18 to 8.19). Most of the isolates were Escherichia coli (77.51%), followed by Klebsiella pneumoniae (20.71%). Eighty-eight (10.41%) of ESBL-E were simultaneous ESBL and carbapenemase (CP) producers, 1.83% in the case of E. coli and 42.86% among K. pneumoniae isolates. Of the ESBL typed, 52.15% belonged to the cefotaximases (CTX-M-15) type and 91.38% of the CP were oxacillinase (OXA-48) type. Only 0.43% patients presented an active infection by ESBL-E at admission.

CONCLUSIONS

The prevalence found in our study is very similar to that found in literature. However, we found a high percentage of simultaneous ESBL and CP producers, particularly in K. pneumoniae. Despite the high prevalence of colonised patients, the ESBL-infection rate at admission was very low.

Detection of Plasmid-Mediated β-Lactamase Genes and Emergence of a Novel AmpC (CMH-1) in Enterobacter cloacae at a Medical Center in Southern Taiwan

The plasmid-mediated extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in Enterobacter spp. have increasingly been reported. In this study, we investigated the prevalence of the plasmid-mediated β-lactamases in Enterobacter cloacae from bloodstream isolates at a medical center in southern Taiwan. ESBL and ampC genes were detected by PCRs and DNA sequencing. Conjugation experiments were conducted to confirm the transferability of the genetic resistance trait. Among 41 non-repetitive blood isolates of cefuroxime-resistant E. cloacae, eight isolates exhibited ESBL phenotype confirmed by double-disk synergistic tests. Nearly all the strains were susceptible to carbapenems. The prevalence rate of the plasmid-mediated bla_ampC genes was 73% (30/41), including one bla_DHA-1, one bla_MIR-6, two novel bla_CMH-1 genes and other bla_ACT-like genes. Coexistence of plasmid-mediated bla_ACT and ESBL genes (10 with bla_SHV-12 and one with bla_CTX-M-3) was observed. Successful transmissions of the bla_ACT and bla_CMH-1 were demonstrated in some transconjugants. The inducible or derepressed CMH-1 had expanded activity of isolates versus ceftazidime. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis and pulsotype showed distinct patterns suggesting non-clonal relationship. In conclusion, plasmid-mediated bla_ACT-likeampC genes in E. cloacae isolates have been highly prevalent in southern Taiwan and may continue genetic evolution, contributing to the complexities in antibiotic-resistant mechanisms.

Pulsed-Field Gel Electrophoresis Used for Typing of Extended-Spectrum-β-Lactamases- Producing Escherichia coli Isolated from Infant ҆S Respiratory and Digestive System

Escherichia coli infections are becoming increasingly difficult to treat because of emerging antimicrobial resistance, mostly to expanded-spectrum cephalosporins, due to the production of extended-spectrum β-lactamases (ESBLs).Despite extensive studies of ESBL- producing E.coli in adult patients, there is a lack of information about the epidemiology and spread of ESBL organisms in pediatric population. The aim of this study was to examine the gastrointestinal tract as an endogenous reservoir for the respiratory tract colonization with ESBL- E. coli in children, hospitalized because of the severity of the respiratory illness. The study group consists of 40 children with ESBL-producing E. coli strains isolated from the sputum and from the rectal samples. A control group of 15 E. coli isolated from rectal swabs of healthy children were included in the analysis. The comparison of the strains was done by using antimicrobial susceptibility patterns of the stains, and pulsed field gel electrophoresis was performed for molecular typing, using XbaI digestion. 90% of the compared pairs of strains in the study group were with identical antimicrobial susceptibility patterns and indistinguishable in 79.2% by the obtained PFGE – profiles.33.3% (5/15) of confirmed E. coli strains from the control group were found to be ESBL – producers. Resulting band profiles of all isolates demonstrated presence of 12 pulsotypes, with 100% similarity within the pulsotypes. Although, some isolates obtained from different patients were genetically indistinguishable, these strains were not hospital acquired, as none of the patients satisfied the criteria for hospital acquired pneumonia, and there was a lack of an obvious transmission chain. All ESBL –E. coli isolated from sputum in clinical cases were obtained from patients under the age of one. According to the resistance profile of the compared pairs and the PFGE comparison of all isolates, it can be concluded that the gastrointestinal tract is the main reservoir of ESBL-E. coli. Small age in infants is a risk factor for translocation of bacteria, enabling the colonization of the respiratory tract.

Survey on pathogenic Escherichia coli and Salmonella spp. in captive cockatiels (Nymphicus hollandicus)

We surveyed healthy captive cockatiels (Nymphicus hollandicus) for Escherichia coli and Salmonella spp. Cloacal swabs were collected from 94 cockatiels kept in commercial breeders, private residencies and pet shops in the cities of São Paulo/SP and Niterói/RJ (Brazil). Three strains of E. coli from each individual were tested for the presence of ExPEC-, APEC- and DEC-related genes. We evaluated the bla_TEM, bla_SHV, bla_OXA, bla_CMY, bla_CTX-M, tetA, tetB, aadA, aphA, strAB, sul1, sul2, sul3, qnrA, qnrD, qnrB, qnrS, oqxAB, aac (6)'-Ib-cr, qepA resistance genes and markers for plasmid incompatibility groups. Salmonella spp. was not detected. E. coli was isolated in 10% of the animals (9/94). Four APEC genes (ironN, ompT, iss and hlyF) were detected in two strains (2/27-7%), and iss (1/27-4%) in one isolate. The highest resistance rates were observed with amoxicillin (22/27-82%), ampicillin (21/27-79%), streptomycin (18/27-67%), tetracycline (11/27-41%). Multiresistance was verified in 59% (16/27) of the isolates. We detected strAB, bla_TEM, tetA, tetB, aadA, aphaA, sul1, sul2, sul3 resistance genes and plasmid Inc groups in 20 (74%) of the strains. E. coli isolated from these cockatiels are of epidemiological importance, since these pets could transmit pathogenic and multiresistant microorganisms to humans and other animals.

Trattamento antibiotico empirico, mirato o ragionato? Dalla pratica clinica alle Linee Guida EAU 2017

Empirical antibiotic treatment of urinary tract infections: from everyday clinical practice to EAU guidelines 2017

Recent epidemiological data confirm the increasing problem of antimicrobial resistance not only for hospitalized, healthcare-associated patients but also for outpatients. In particular, the progressive increase in resistance to broad-spectrum antibiotics, such as third-generation cephalosporins, fluoroquinolones, or carbapenems in Enterobacteriaceae, is an alarming situation for all urologists and general practitioners. The management of uncomplicated urinary tract infections are an important step in antibiotic stewardship achievement: a new approach is urgently required. All international Guidelines on urological infections suggest to take into account the following parameters for choosing antimicrobial therapy: spectrum and susceptibility patterns of the aetiological pathogens; efficacy for the particular indication in clinical studies; tolerability and adverse reactions; adverse ecological effects; costs and availability. In other words, an accurate evaluation of all patients and bacteria-related factors should be performed, along with the consideration of local data of bacterial resistance rate. According to these principles and the available susceptibility patterns in Italy, fosfomycin trometamol 3 g single dose and nitrofurantoin, are considered as drugs of first choice.

Antibiotic resistance in travellers' diarrhoeal disease, an external perspective

BACKGROUND

There are many recommendations on the use of antibiotics for prophylaxis and treatment of travellers' diarrhoea (TD). As pharmacists with a special interest in antimicrobial stewardship, we examine and offer our perspective on advice that is recommended to travellers in terms of prevention, treatment and management of TD with a focus on antibiotic use and resistance.

METHODS

Publications on TD were identified through PubMed, Google Scholar and Cochrane Library databases searches using search terms 'travellers diarrhoea', 'travellers diarrhoea', 'travellers' diarrhoea' 'guidelines', 'expert opinion', 'expert reviews', 'South Asia' and 'South East Asia' (S and SE Asia), 'antibiotics', 'resistance genes', 'travel advice', 'pharmacists', 'guidelines', 'prevention' and 'treatment'. References of articles were also screened for additional relevant studies.

RESULTS

Whilst most guidelines and expert reviews were in agreement with the restricted use of antibiotics unless there was a clinical need, the literature review identified gaps in research into behaviours of travellers regarding non-compliance with the pre-travel advice provided and the need for in depth training and education for all healthcare professionals in providing 'tailored' advice for travellers going to high-risk destinations.

CONCLUSIONS

Travellers should be made aware of the problems of antimicrobial resistance in their destination and home countries and offered alternative forms of prophylaxis for TD. Strategies for prevention of TD, other than the use of antibiotics, also need to be emphasized. All healthcare professionals involved in giving advice about TD should be familiar with the epidemiology of the condition as this will inform responsible behaviours, risk assessment and management strategies in different geographical areas.

Prevalence of Virulence Genes in Extended-Spectrum β-lactamases (ESBLs)-Producing Salmonella in Retail Raw Chicken in China

Extended-spectrum β-lactamases (ESBLs)-producing Salmonella is a tremendous hazard to food safety and public health. The objective of this study was to determine the prevalence of 30 virulence genes (avrA, sipA, sseC, marT, rhuM, siiE, pipA, pipD, envR, gogB, gtgA, sodC1, sseI, irsA, sopE2, spvC, rck, spvR, fhuA, msgA, pagK, srfj, stkc, fimA, lpfD, pefA, stcC, steB, stjB, and tcfA) in 156 ESBLs-producing Salmonella isolates that belonged to 21 serotypes. These isolates were recovered from retail raw chicken samples collected from 5 provinces and 2 national cities in China between 2007 and 2012. The results indicated that 154 (98.7%) ESBLs-producing Salmonella isolates carried at least 1 virulence gene, 138 (88.5%) simultaneously carried at least 5 virulence genes, 107 (68.6%) carried 10 or more, and 20 (12.8%) carried 15 or more virulence genes. The most frequently detected virulence genes were marT (n = 127, 81.4%), siiE (n = 126, 80.8%), msgA (n = 121, 77.6%), and sipA (n = 121, 77.6%). Significant difference was identified between detection percentages of virulence genes of rhuM, pipD, envR, sopE2, pagK, lpfD, steB, and stjB in S. Indiana, S. Thompson, S. Enteritidis, S. Typhimurium, S. Shubra, S. Edinburg, and S. Agona isolates. Distribution of virulence genes were significantly influenced by sampling districts (P < 0.01), especially for sodC1 and pipD, and then were msgA and sopE2. The heatmap showed the frequencies of virulence genes in ESBLs-producing isolates from retail chickens in southern, central, and northern regions of China were completely different from each other. Based on our findings, ESBLs-producing Salmonella of retail chicken origin were common carriers of multiple virulence genes and were regionally distributed.

Phenotypic Detection of Extended Spectrum Beta lactamase and Carbapenemase Co-producing Clinical Isolates from Two Tertiary Hospitals in Kano, North West Nigeria

BACKGROUND

Continue rise in unprofessional use of antibiotics in our hospitals and communities is worrisome. A research study was therefore conducted to detect extended spectrum beta-lactamase (ESBL), carbapenemase, metallobeta lactamase and their co-production phenotypically from isolates obtained from patients admitted to or attending two tertiary hospitals in Kano, Nigeria.

METHOD

A total of 248 isolates of Escherichia coli and Klebsiella pneumoniaewere screened phenotypically for ESBL production and carbapenemase production according to CLS1 2012 breakpoints using double disk synergy test and modified Hodge test (MHT) respectively. Antibiotic susceptibility of the organisms was tested against colistin, tigecycline and 3 flouroquinolones.

RESULTS

The result shows that 58.0% of the isolates were ESBL producers with higher percentage in K. pneumoniae (62.9%). Further, about 40.3% and 36.6% of the isolates were resistant to meropenem and imipenem respectively. However, E. coli showed higher resistance to meropenem (47.1%) while K. pneumoniae showed higher resistance to imipenem (44.4%). Co-productions of carbapenemase and ESBL were observed in both E. coli and K. pneumoniae. Carbapenemase producing isolates were more obtained from uro-pathogens and wound isolates, with almost all the cases of co-production of the β lactamases occurring in urine and cathertips isolates. Overall susceptibilities of the isolates to colistin and tigecycline were 64.6and70.0% respectively, but isolates were less susceptible to flouroquinolones.

CONCLUSION

The finding of the study therefore indicates that carbapenem resistance is mediated by carbapenemase production and or overproduction of ESBL coupled with reduced porins. Co-production of carbapenemase, MBLs and ESBLs by some of the isolates is worrisome. Susceptibility to colistin and tigecycline was still promising, but increasing resistance to flouroquinolones has been observed.

Prevalence of extended-spectrum-β-lactamase-producing Enterobacteriaceae: first systematic meta-analysis report from Pakistan

Background

South-Asia is known as a hub for multidrug-resistant (MDR) bacteria. Unfortunately, proper surveillance and documentation of MDR pathogens is lacking in Pakistan. The alarming increase in the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a serious problem. From this perspective, we analysed published data regarding ESBL-producing Enterobacteriaceae in different regions of Pakistan.

Methods

A meta-analysis was performed to determine the prevalence of ESBL-producing Enterobacteriaceae in Pakistan. A Web-based search was conducted in electronic databases, including PubMed, Scopus and PakMedi Net (for non-indexed Pakistani journals). Articles published (in either indexed or non-indexed journals) between January 2002 and July 2016 were included in the study. Relevant data were extracted, and statistical analysis was performed using the Metaprop command of STATA version 14.1.

Results

A total of 68 studies were identified from the electronic data base search, and 55 of these studies met our inclusion criteria. Pakistan’s overall pooled proportion of ESBL-producers was 0.40 (95% CI: 0.34–0.47). The overall heterogeneity was significant (I2 = 99.75%, p < 0.001), and significant ES = 0 (Z = 18.41, p < 0.001) was found. OXA, SHV, TEM and CTX-M were the most commonly found gene variants for ESBLs in these studies.

Conclusion

The prevalence of ESBL-producing Enterobacteriaceae is high in Pakistan. Little is known about the annual frequency of ESBLs and their prevalence in different provinces of Pakistan. No data are available regarding ESBL frequency in Baluchistan. This underscores an urgent demand for regular surveillance to address this antimicrobial resistance problem. Surveillance to better understand the annual ESBL burden is crucial to improve national and regional guidelines.

Molecular detection of β-lactamase and integron genes in clinical strains of Klebsiella pneumoniae by multiplex polymerase chain reaction

INTRODUCTION:

Infections caused by β-lactamase-producing gram-negative bacteria, such as Klebsiella pneumoniae, are increasing globally with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the prevalence of antibiotic resistance genes (β-lactamase and integron genes) using multiplex PCR.

METHODS

One-hundred K. pneumoniae isolates were collected from different clinical samples. Antibiotic susceptibility testing was performed with thirteen different antibiotics. Multiplex-PCR was used to detect β-lactamase (bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC) and integron genes (int I, int II, and int III).

RESULTS:

The highest and lowest rate of resistance was exhibited against amikacin (93%) and imipenem (8%), respectively. The frequency of β-lactamase-positive K. pneumoniae was 37%, and the prevalence of the bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC genes was 38%, 24%, 19%, 12%, 6%, 11%, 33%, 0%, 28%, and 23%, respectively. Of the 100 isolates, eight (8%) were positive for class I integrons; however, class II and III integrons were not detected in any of the strains.

CONCLUSIONS:

These results indicate co-carriage of a number of β-lactamase genes and antibiotic resistance integrons on the same plasmids harboring multi-drug resistance genes. It seems that these properties help to decrease treatment complications due to resistant bacterial infections by rapid detection, infection-control programs and prevention of transmission of drug resistance.

Incidence of Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli and Klebsiella Infections in the United States: A Systematic Literature Review

BACKGROUND

Despite a reported worldwide increase, the incidence of extended-spectrum β-lactamase (ESBL) Escherichia coli and Klebsiella infections in the United States is unknown. Understanding the incidence and trends of ESBL infections will aid in directing research and prevention efforts.

OBJECTIVE

To perform a literature review to identify the incidence of ESBL-producing E. coli and Klebsiella infections in the United States.

DESIGN

Systematic literature review.

METHODS

MEDLINE via Ovid, CINAHL, Cochrane library, NHS Economic Evaluation Database, Web of Science, and Scopus were searched for multicenter (≥2 sites), US studies published between 2000 and 2015 that evaluated the incidence of ESBL-E. coli or ESBL-Klebsiella infections. We excluded studies that examined resistance rates alone or did not have a denominator that included uninfected patients such as patient days, device days, number of admissions, or number of discharges. Additionally, articles that were not written in English, contained duplicated data, or pertained to ESBL organisms from food, animals, or the environment were excluded.

RESULTS

Among 51,419 studies examined, 9 were included for review. Incidence rates differed by patient population, time, and ESBL definition and ranged from 0 infections per 100,000 patient days to 16.64 infections per 10,000 discharges and incidence rates increased over time from 1997 to 2011. Rates were slightly higher for ESBL-Klebsiella infections than for ESBL-E. coli infections.

CONCLUSION

The incidence of ESBL-E. coli and ESBL-Klebsiella infections in the United States has increased, with slightly higher rates of ESBL-Klebsiella infections. Appropriate estimates of ESBL infections when coupled with other mechanisms of resistance will allow for the appropriate targeting of resources toward research, drug discovery, antimicrobial stewardship, and infection prevention.

Infect Control Hosp Epidemiol 2017;38:1209–1215

Microbiology of surgical site infections in patients with cancer: A 7-year review

BACKGROUND

Health care-associated infections (HAIs) have arisen as major sources of multidrug-resistant bacteria. Surgical site infections (SSIs) are the most frequent HAIs in many countries, with high antimicrobial-resistant prevalence.

METHODS

A 7-year retrospective review (2008-2014) of microbiologic data within a prospective surveillance program on patients with SSI at a cancer hospital in Mexico.

RESULTS

There were 23,421 surgeries performed during the study period. The SSI rate was 7.9%. Gram-negative bacilli (GNB) were found in 56.5% of samples. Escherichia coli was the most frequent microorganism (27.5%), followed by Staphylococcus aureus (16.3%). SSI caused by S aureus showed a decreasing trend (P = .04). Extended-spectrum β-lactamase (ESBL)-producing E coli increased from 39.5% in 2008 to 72.5% in 2014 (P < .001). Fluoroquinolone resistance also increased in all members of the Enterobacteriaceae. Methicillin-resistant S aureus (MRSA) was isolated in 32% of cases with no significant increase (P value is not significant).

CONCLUSIONS

GNB caused most SSIs, with an increase of ESBL E coli strains. In breast and thoracic surgery, S aureus remained the most frequent isolate. MRSA remained stable throughout the study period. We observed a decreasing trend in S aureus. These findings show the differences in the microbiology of SSIs in a middle-income country and the increasing trend of ESBL enterobacteria and other multidrug-resistant organisms, such as Enterococcus faecium.

Antibiotic Resistance and Virulence Phenotypes of Recent Bacterial Strains Isolated from Urinary Tract Infections in Elderly Patients with Prostatic Disease

Acute bacterial prostatitis is one of the frequent complications of urinary tract infection (UTI). From the approximately 10% of men having prostatitis, 7% experience a bacterial prostatitis. The purpose of this study was to investigate the prevalence of uropathogens associated with UTIs in older patients with benign prostatic hyperplasia and to assess their susceptibility to commonly prescribed antibiotics as well as the relationships between microbial virulence and resistance features. Uropathogenic Escherichia coli was found to be the most frequent bacterial strain isolated from patients with benign prostatic hyperplasia, followed by Enterococcus spp., Enterobacter spp., Klebsiella spp., Proteus spp., Pseudomonas aeruginosa, and Serratia marcescens. Increased resistance rates to tetracyclines, quinolones, and sulfonamides were registered. Besides their resistance profiles, the uropathogenic isolates produced various virulence factors with possible implications in the pathogenesis process. The great majority of the uropathogenic isolates revealed a high capacity to adhere to HEp-2 cell monolayer in vitro, mostly exhibiting a localized adherence pattern. Differences in the repertoire of soluble virulence factors that can affect bacterial growth and persistence within the urinary tract were detected. The Gram-negative strains produced pore-forming toxins-such as hemolysins, lecithinases, and lipases-proteases, siderophore-like molecules resulted from the esculin hydrolysis and amylases, while Enterococcus sp. strains were positive only for caseinase and esculin hydrolase. Our study demonstrates that necessity of investigating the etiology and local resistance patterns of uropathogenic organisms, which is crucial for determining appropriate empirical antibiotic treatment in elderly patients with UTI, while establishing correlations between resistance and virulence profiles could provide valuable input about the clinical evolution and recurrence rates of UTI.

Characterisation of extended-spectrum β-lactamase and AmpC β-lactamase-producing Enterobacteriaceae isolated from companion animals in New Zealand

AIMS

To assess the occurrence of, and characterise, extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase (AmpC)-producing Enterobacteriaceae isolated by veterinary diagnostic laboratories from infection sites in companion animals in New Zealand.

METHODS

Selected Enterobacteriaceae isolates were submitted by seven New Zealand veterinary diagnostic laboratories. They were isolated from infection sites in companion animals between June 2012 and June 2013, and were resistant to amoxicillin-clavulanic acid, fluoroquinolones, or any combination of two or more antimicrobials. Based on disk diffusion test results, the isolates were phenotypically categorised according to production of ESBL and AmpC. Genes for ESBL and AmpC production were amplified by PCR and sequenced. Escherichia coli isolates were also typed by multilocus sequence typing.

RESULTS

A total of 115 isolates matching the inclusion criteria were obtained from the participating laboratories, of which 74 (64%) originated from dogs and 29 (25%) from cats. Seven bacterial species were identified, of which E. coli was the most common (87/115, 76%). Of the 115 isolates, 10 (9%) expressed the ESBL phenotype, 43 (37%) the AmpC phenotype, and seven (6%) both ESBL and AmpC phenotypes. Of the 60 ESBL and AmpC-producing isolates, 36 (60%) were E. coli. Amongst these isolates, 27/60 (45%) were classified as multidrug resistant, compared with 15/55 (27%) non-ESBL or AmpC-producing isolates (p<0.01). Ninety five isolates were resistant to amoxicillin-clavulanic acid and 58 (61%) of these were ESBL or AmpC-producing. The predominant ESBL genes were bla_CTX-M-14 and bla_CTX-M-15, and the dominant plasmid-encoded AmpC gene was bla_CMY-2. Thirty-eight E. coli multilocus sequence types (ST) were identified, and the most prevalent were ST12 (12/89, 13%), ST131 (6/89, 7%) and ST648 (6/89, 7%). ESBL and AmpC-producing isolates accounted for 35/1,082 (3.2%) of the Enterobacteriaceae isolated by one laboratory network over the study period.

CONCLUSIONS AND CLINICAL RELEVANCE

ESBL and AmpC-producing Enterobacteriaceae were associated with clinical infections in companion animals in New Zealand, and were often multidrug resistant. In this study, these organisms accounted for <5% of all Enterobacteriaceae isolated from infection sites by one laboratory network, but their prevalence among isolates resistant to amoxicillin-clavulanic acid was 61%. Therefore routine secondary testing for ESBL and AmpC production by Enterobacteriaceae that are resistant to amoxicillin-clavulanic acid in primary testing could improve the accuracy of definitive antimicrobial therapy in companion animals in New Zealand.

Prevalence and Diversity of Salmonella Serotypes in Ecuadorian Broilers at Slaughter Age

Salmonella is frequently found in poultry and represent an important source for human gastrointestinal infections worldwide. The aim of this study was to investigate the prevalence, genotypes and antimicrobial resistance of Salmonella serotypes in broilers from Ecuador. Caeca content from 388 at random selected broiler batches were collected in 6 slaughterhouses during 1 year and analyzed by the ISO 6579/Amd1 protocol for the isolation for Salmonella. Isolates were serotyped and genotypic variation was acceded by pulsed field gel electrophoresis. MIC values for sulfamethoxazole, gentamicin, ciprofloxacin, ampicillin, cefotaxime, ceftazidime, tetracycline, streptomycin, trimethropim, chloramphenicol, colistin, florfenicol, kanamycin and nalidixic acid were obtained. Presence of blaCTX-M, blaTEM, blaSHV and blaCMY; and mcr-1 plasmid genes was investigated in resistant strains to cefotaxime and colistin respectively. Prevalence at batch level was 16.0%. The most common serotype was S. Infantis (83.9%) followed by S. Enteritidis (14.5%) and S. Corvallis (1.6%). The pulsed field gel electrophoresis analysis showed that S. Corvallis, S. Enteritidis and S. Infantis isolates belonged to 1, 2 and 12 genotypes respectively. S. Infantis isolates showed high resistance rates to 12 antibiotics ranging from 57.7% (kanamycin) up to 98.1% (nalidixic acid and sulfamethoxazole). All S. Enteritidis isolates showed resistance to colistin. High multiresistant patterns were found for all the serotypes. The blaCTX-M gene was present in 33 S. Infantis isolates while mcr-1 was negative in 10 colistin resistant isolates. This study provides the first set of scientific data on prevalence and multidrug-resistant Salmonella coming from commercial poultry in Ecuador.

HIGH PREVALENCE OF MULTI-DRUG RESISTANT KLEBSIELLA PNEUMONIAE IN A TERTIARY TEACHING HOSPITAL IN WESTERN KENYA

INTRODUCTION

Klebsiella pneumoniae is a gram negative enterobacteriaciae commonly associated with nosocomial infections. Multidrug resistant strains are increasingly being reported with corresponding increase in morbidity and mortality. The study outlines the epidemiology and antibiotic resistance pattern of K. pneumonia over a 10 year period in Moi Teaching and Referral Hospital, Eldoret, Kenya.

METHODOLOGY AND STUDY DESIGN

This is a retrospective analysis of all the blood culture results for K. pneumoniae isolates in the hospital for the period 2002-2013.

RESULTS

K. pneumoniae accounted for 23% of the hospital isolates (231/1356) during the study period; of these, 82.6% were from the New Born Unit. Most of the isolates were multi drug resistant with highest resistance of over 80% to Penicillins, Cephalosporins, Macrolides, Tetracyclines, Sulphonamides, Lincosamides and Chloramphenicol. Aminoglycoside and Quinolone resistance was also high at 49.2% and 41.3% respectively. The lowest resistance rates were documented for Carbapenems (23.2%). For specific antibiotics, there was high resistance to commonly used antibiotics (over 80% for Ceftriaxone, Cefipime, Gentamycin and Ceftazidime). The antibiotics with least resistance were Amikacin and Meropenem (21% and 7 % respectively).

CONCLUSION

There was a high prevalence of multidrug resistant K. pneumoniae isolates in the hospital, the majority originated from the New Born Unit. Resistance to third generation Cephalosporins and Gentamycin was high while Meropenem and Amikacin had the least resistance.