Clinical profiles of patients colonized or infected with extended-spectrum beta-lactamase producing Enterobacteriaceae isolates: a 20 month retrospective study at a Belgian University Hospital

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

For antimicrobial resistance (AMR) surveillance, it is important not only to detect AMR genes, but also to determine their plasmidic or chromosomal location, as this will impact their spread differently. Whole-genome sequencing (WGS) is increasingly used for AMR surveillance. However, determining the genetic context of AMR genes using only short-read sequencing is complicated. The combination with long-read sequencing offers a potential solution, as it allows hybrid assemblies. Nevertheless, its use in surveillance has so far been limited. This study aimed to demonstrate its added value for AMR surveillance based on a case study of extended-spectrum beta-lactamases (ESBLs). ESBL genes have been reported to occur also on plasmids. To gain insight into the diversity and genetic context of ESBL genes detected in clinical isolates received by the Belgian National Reference Center between 2013 and 2018, 100 ESBL-producing Shigella and 31 ESBL-producing Salmonella were sequenced with MiSeq and a representative selection of 20 Shigella and six Salmonella isolates additionally with MinION technology, allowing hybrid assembly. The bla CTX-M-15 gene was found to be responsible for a rapid rise in the ESBL Shigella phenotype from 2017. This gene was mostly detected on multi-resistance-carrying IncFII plasmids. Based on clustering, these plasmids were determined to be distinct from the circulating plasmids before 2017. They were spread to different Shigella species and within Shigella sonnei between multiple genotypes. Another similar IncFII plasmid was detected after 2017 containing bla CTX-M-27 for which only clonal expansion occurred. Matches of up to 99 % to plasmids of various bacterial hosts from all over the world were found, but global alignments indicated that direct or recent ESBL-plasmid transfers did not occur. It is most likely that travellers introduced these in Belgium and subsequently spread them domestically. However, a clear link to a specific country could not be made. Moreover, integration of bla CTX-M in the chromosome of two Shigella isolates was determined for the first time, and shown to be related to ISEcp1. In contrast, in Salmonella, ESBL genes were only found on plasmids, of which bla CTX-M-55 and IncHI2 were the most prevalent, respectively. No matching ESBL plasmids or cassettes were detected between clinical Shigella and Salmonella isolates. The hybrid assembly data allowed us to check the accuracy of plasmid prediction tools. MOB-suite showed the highest accuracy. However, these tools cannot replace the accuracy of long-read and hybrid assemblies. This study illustrates the added value of hybrid assemblies for AMR surveillance and shows that a strategy where even just representative isolates of a collection used for hybrid assemblies could improve international AMR surveillance as it allows plasmid tracking.

Intestinal Carriage of Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae in Hemodialysis Patients

Background: Gastrointestinal colonization with resistant pathogens is significant because they could be easily transmitted to other hosts or spread to different microbiota through mobile genetic elements. Objectives: This study assessed the prevalence of fecal carriage of extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE, respectively) among hemodialysis patients and the factors affecting its occurrence in a hospital in Tehran. Methods: From January 2018 to May 2019, 150 hemodialysis patients referred to a hospital in Tehran were sampled in this study. Stool samples of the patients were diluted in saline and cultured on MacConkey agar plates containing cefotaxime, ceftazidime, imipenem, and meropenem discs. The clinical data were analyzed to identify the risk factors using a logistic regression model. Results: The colonization rate of ESBL-E was 48.6%, while only 2% of patients were identified as the carriers of CPE (3 of 150). A higher prevalence rate was obtained for intestinal carriage of ESBL-E among hemodialysis patients aged 18 to 42 years using multivariate analysis. The prevalence rate of multidrug-resistant isolates was 73.8%. The blaCTX-M1 gene was identified as the most prevalent ESBL gene. Among carbapenemase-encoding genes, blaKPC and blaoxa-48 were found in 12 and two isolates, respectively. Conclusions: These results demonstrated a high prevalence rate of ESBLs among hemodialysis patients, although this rate was low for carbapenemases. Therefore, more control measures should be taken in hospitals to prevent the spread of antibiotic resistance genes in healthcare settings.

Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms

Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.

Time trend of prevalence and susceptibility to nitrofurantoin of urinary MDR Escherichia coli from outpatients

OBJECTIVES

To assess the time trend of the prevalence of urinary MDR Escherichia coli in Belgian outpatients (2005 versus 2011-12), the antibiotic susceptibility of urinary MDR E. coli, and the time trend of non-susceptibility to nitrofurantoin, i.e. first-line treatment for uncomplicated urinary tract infections (UTIs), of urinary MDR E. coli (2005 versus 2011-12).

METHODS

In this secondary analysis of a multicentre study, which collected a convenience sample of voluntary participating laboratories (15 and 8 in 2005 and 2011-12, respectively), we analysed antimicrobial susceptibilities (ampicillin, amoxicillin/clavulanate, cefalotin, ciprofloxacin, nitrofurantoin and trimethoprim/sulfamethoxazole) of urinary E. coli. MDR was defined as resistance to three or more of these agents. The prevalence of MDR E. coli and its non-susceptibility to nitrofurantoin was compared between 2005 and 2011-12 using a generalized estimating equation model.

RESULTS

MDR status could be determined for 9704 and 12512 urinary E. coli isolates from 7911 and 9441 patients in 2005 and 2011-12, respectively, with most patients being women (79% in both study periods). The prevalence of MDR increased from 28.4% (2758/9704) in 2005 to 34.3% (4286/12512) in 2011-12 (adjusted OR 1.305; 95% CI 1.220-1.397). Within the MDR isolates, the prevalence of nitrofurantoin non-susceptibility decreased from 23.2% (623/2684) in 2005 to 10.7% (455/4253) in 2011-12 (adjusted OR 0.424; 95% CI 0.363-0.494).

CONCLUSIONS

Despite a high prevalence of MDR E. coli in urinary samples from Belgian outpatients, nitrofurantoin could still be recommended as first-line empirical treatment in uncomplicated UTIs.

Diversity, Virulence, and Clinical Significance of Extended-Spectrum β-Lactamase- and pAmpC-Producing Escherichia coli From Companion Animals

Escherichia coli are opportunistic pathogens with the potential to cause a variety of infections in both humans and animals and in many cases have developed antimicrobial resistance. In this study, we characterized extended-spectrum cephalosporin resistant (ESCR) E. coli isolates from diseased companion animals (dogs, cats, and horses) and related the results to clinical findings. ESCR E. coli clinical isolates obtained over a 6-year period were screened for extended-spectrum β-lactamase (ESBL) and/or plasmid mediated AmpC (pAmpC) and virulence markers likely to be associated with extraintestinal pathogenic E. coli (ExPEC). ESBL and/or pAmpC genetic determinants were identified in 79.9% of the ESCR E. coli isolates with bla CTX-M genes being the most common ESBL genotype of which bla CTX-M-15, bla CTX-M-14, and bla CTX-M-55 were the most prevalent. In addition, bla CMY -2 was the most common genotype identified amongst pAmpC producing isolates. Phylogenetic group typing showed that B2 was the most prevalent phylogroup among the ESCR E. coli isolates, followed by the closely related phylogroups D and F which are also associated with extra-intestinal infections. ESCR was also identified in phylogroups commonly regarded as commensals (B1, A, and C). Virulence factor (VF) scores >2 were mostly present amongst isolates in phylogroup B2. Higher virulence scores were found in isolates lacking ESBL/pAmpC resistance genes compared with those carrying both genes (p < 0.05). Five of phylogroup B2 isolates, were typed to the pandemic virulent O25b-ST131 clone and three ST131 isolates carrying bla CTX-M-15 belonged to the subclade C2/H30Rx whilst one isolate carrying bla CTX-M-27 typed to the recently described sub-clade C1-M27. MLST typing also identified other sequence types commonly associated with infections in humans (ST410, ST10, and ST648). Most ESCR E. coli isolates obtained in pure growth were cultured from normally sterile body sites (mostly from urinary tract infections, UTIs) whilst only a small proportion were obtained from body sites populated with commensal flora (p < 0.0001). Our study has shown that ExPEC ESBL/pAmpC producing E. coli isolates are common amongst companion animal isolates and are associated with colonization and infection. In addition, their isolation from a normally sterile site is likely to be clinically significant and warrants antimicrobial treatment.

Prevalence and risk factors for colonization by extended-spectrum β-lactamase-producing or ST 131 Escherichia coli among asymptomatic adults in community settings in Southern Taiwan

Purpose: Fecal carriage of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) is common in Asia, especially in China and Southeast Asia. There are no data about fecal carriage of ESBL-EC and mcr-1-positive E. coli in Taiwan, and few studies focusing on the risk factors of asymptomatic fecal carriage of epidemic ST131 E. coli have been published.

Patients and methods: From healthy inhabitants attending health examinations at a medical center in southern Taiwan in 2017, we collected 724 stool samples, which were examined for ESBL-EC fecal carriage using chromogenic medium. ST131 and mcr1-positive E. coli were also investigated using multiplex PCR. Clinical data from all participating adults were collected to analyze the risk factors for fecal ESBL-EC or ST131 E. coli carriage.

Results: The prevalence rate of asymptomatic ESBL-EC fecal carriage in adults was 1.9% (14/724). ST131 was found in 22 (3.0%) adults and mcr-1-positive E. coli was found in three (0.4%) adults. A multivariate analysis showed that the risk factors associated with ESBL-EC carriage were diabetes mellitus (adjusted odds ratio [aOR]: 5.5, 95% confidence interval [CI]: 1.3–22.7), a history of colonic polyps (aOR: 6.4, 95% CI: 1.6–24.9), and chronic renal insufficiency (aOR: 20.7, 95% CI: 1.4–305.7). Underlying cancer (aOR: 4.8, 95% CI: 1.0–22.5) and stroke (aOR: 18.0, 95% CI: 1.6–207.5) were associated with ST131 E. coli fecal carriage. In our cohort, travel to Asian countries and food habit were not associated with ST131 or ESBL-EC fecal carriage.

Conclusions: The ESBL-EC or ST131 E. coli fecal carriage rate is low among asymptomatic adults in Taiwan. Certain underlying medical conditions were associated with their fecal carriage.

Disparity of the "screen-and-isolate" policy for multidrug-resistant organisms: A national survey in French adult ICUs

BACKGROUND

The prevalence of multidrug-resistant organisms (MDROs) has dramatically increased. The aim of this survey was to describe and analyze the different screening and isolation policies regarding MDROs in French adult intensive care units (ICUs).

MATERIALS AND METHODS

A multicenter online survey was performed among French ICUs, including 63 questions distributed into 4 parts: characteristics of the unit, MDRO screening policy, policy regarding contact precautions, and ecology of the unit.

RESULTS

From April 2015 to June 2016, 73 of 301 ICUs (24%) participated in the survey. MDRO screening was performed on admission in 96% of ICUs, for at least 1 MDRO (78%). MDRO screening was performed weekly during ICU stay in 83% of ICUs. Preemptive isolation was initiated on admission in 82% of ICUs, mostly in a targeted way (71%). Imported and acquired MDRO rates >10% were reported in 44% and 27% of ICUs, respectively. An MDRO outbreak had occurred within the past 3 years in 48% of cases.

CONCLUSION

French ICUs have variable screening and isolation approaches for MDROs, as up to 10 combinations were met. Discrepancies with the 2009 national guidelines were observed. Very few ICUs practice without some form of screening and isolation of patients upon admission.

Maternal vaginal colonization with selected potential pathogens of neonatal sepsis in the era of antimicrobial resistance, a single center experience from Sri Lanka

BACKGROUND

Maternal vaginal colonization with antibiotic resistant organisms is a growing concern in countries with high antibiotic resistance rates.

METHODS

A low vaginal swab was collected from mothers on admission, on discharge and a peri-rectal swab was collected from the neonates born to these mothers on discharge. Routine microbiological methods were used to identify the colonization rates for Escherichia coli, Klebsiella spp. and Streptococcus agalactiae.

RESULTS

The pre-delivery colonization rate among the 250 participants for total Enterobacteriaceae was 18.8%. The colonization rates for Klebsiella spp., E. coli and S. agalactiae were, 12.4, 5.6 and 14.8% respectively. Two Klebsiella spp. and two E. coli isolates were confirmed to be exentend spectrum β lactamase (ESBL) producers with the commonest resistant determinant being blaCTX-M. Post-delivery swabs were collected from 130 participants and the colonization rates were 41.5% for Enterobacteriaceae, 25.4% for Klebsiella spp., 10.8% for E. coli, and 10.8% for S. agalacteiae. Three Klebsiella isolates and one E. coli isolate were confirmed to be ESBL producers with the commonest resistant determinant being blaCTX-M. Considering the 130 participants with both samples, there was a significant increase in the colonization with any Enterobacteriaceae and Klebsiella spp. (p < 0.05). Peri-rectal swabs were collected from neonates in 159 instances. The isolation rates for Enterobacteriaceae was 34%. The genus specific isolation rate for Klebsiella was 21.4% while the rates for E. coli and S.agalactiae were 10.1 and 5.7% respectively. Two of the E. coli were confirmed to be ESBL producers while none of the klebsiellae were identified to be so. Considering these 159 instances where both the mother and baby were sampled, random amplification of polymorphic DNA (RAPD) analysis revealed that Enterbacteriaceae with same strain type was present in 6.9% of the instances, indicating possible transfer between the mother and neonate. The transfer rate for ESBL producers were 0.6%.

CONCLUSIONS

The lower level of antimicrobial resistance among these potentially community acquired isolates is encouraging. However, in view of the increasing level of resistance reported elsewhere in the region, regular monitoring is warranted.

Epidemiology and Risk Factors for Isolation of Multi-Drug-Resistant Organisms in Patients with Complicated Intra-Abdominal Infections

BACKGROUND

Patients with complicated intra-abdominal infections (cIAIs) caused by multi-drug-resistant organisms (MDROs) have been identified as being at increased risk for adverse outcomes. Prompt identification and stratification of these patients is essential in the clinical management, allowing the physician timely optimization of empiric antimicrobial therapy while awaiting results of intra-operative cultures to streamline antibiotic treatment.

METHODS

The study is a secondary analysis from two prospective multi-center color surveillance studies. It included all consecutively hospitalized adult patients undergoing surgical procedures, interventional drainage, or conservative treatment with cIAIs, with positive cultures performer on intra-operative samples of peritoneal fluid or purulent exudate/discrete abscesses. Patients with pancreatitis and primary peritonitis were excluded. A case-control approach has been used to evaluate the factors associated with the isolation of a MDRO in enrolled patients.

RESULTS

Among 1986 patients included in the study, a total of 3534 micro-organisms were isolated from intra-peritoneal fluid samples; in 46.5% of cultures, two or more pathogens were identified. The MDROs represented 9.8% of the total of isolated micro-organisms. The overall incidence rate of MDROs was 13.9%. The MDROs were more frequently isolated in patients with health-care-associated cIAIs (25.4%). Multi-nomial logistic regression analysis of risk factors demonstrated that statistically significant risk factors independently associated with the occurrence of MDROs were previous antimicrobial therapy administered within seven days before operation, presence of severe cardiovascular disease, white blood cell count <4000/mL or >12,000/mL, cIAI acquired in a healthcare setting, and inadequate source control.

CONCLUSIONS

The study showed that knowledge of five easily recognizable variables-assessable on hospital admission or as soon as the surgical intervention is concluded-might guide the surgeon to identify patients with cIAIs caused by MDROs, and therefore to choose the most adequate empiric antimicrobial therapy for them.

Impact of Discontinuing Contact Precautions for MRSA and ESBLE in an Intensive Care Unit: A Prospective Noninferiority Before and After Study

OBJECTIVE

To compare incidence densities of methicillin-resistant Staphylococcus aureus (MRSA) or extended-spectrum β-lactamase–producing Enterobacteriaceae (ESBLE) acquisition in the intensive care unit (ICU) before and after discontinuation of contact precautions (CP) and application of standard precautions (SP).

DESIGN

Prospective noninferiority before-and-after study comparing 2 periods: January 1, 2012, to January 31, 2014 (the CP period) and February 1, 2014, to February 29, 2016 (the SP period).

SETTING

A 16-bed polyvalent ICU in France with only single-bed rooms with dedicated equipment and reusable medical devices.

PATIENTS

All patients admitted to the ICU during the CP and SP periods were included: 1,547 and 1,577 patients, respectively.

METHODS

Incidence densities of ICU-acquired MRSA or ESBLE were determined per 1,000 patient days. Other studied factors included (1) patient characteristics, (2) incidence densities of MRSA or ESBLE carried at admission, (3) compliance with hand hygiene protocols, and (4) antibiotic consumption.

RESULTS

Incidence densities of ICU-acquired MRSA were 0.82 (95% confidence interval [CI], 0.31–1.33) and 0.79 (95% CI, 0.30–1.29) per 1,000 patient days during the CP and SP periods, respectively. For ESBLE, values were 2.7 (95% CI, 1.78–3.62) and 2.06 (95% CI, 1.27–2.86) per 1,000 patient days. These rates were significantly nonsuperior during the SP period compared to CP period, with a margin of 1 per 1,000 patient days for both MRSA (P=.002) and ESBLE (P=.004). Other factors were comparable during the 2 periods. Only ESBLE carried at admission was inferior during the SP period. We observed a high level of compliance to hand hygiene protocols.

CONCLUSIONS

Discontinuing CP did not increase acquired MRSA and ESBLE in our ICU with single rooms with dedicated equipment, strict application of hand hygiene, medical and paramedical leadership, and good antibiotic stewardship.

Infect Control Hosp Epidemiol 2017;38:1342–1350

Universal versus targeted additional contact precautions for multidrug-resistant organism carriage for patients admitted to an intensive care unit

BACKGROUND

Although additional contact precautions (ACPs) are routinely used to reduce cross-transmission of multidrug-resistant organisms (MDROs), the relevance of isolation precautions remains debated. We hypothesized that the collection of recognized risk factors for MDRO carriage on intensive care unit (ICU) admission might be helpful to target ACPs without increasing MDRO acquisition during ICU stays, compared with universal ACPs.

MATERIALS AND METHODS

This is a sequential single-center observational study performed in consecutive patients admitted to a French medical and surgical ICU. During the first 6-month period, screening for MDRO carriage and ACPs were performed in all patients. During the second 6-month period, screening was maintained, but ACP use was guided by the presence of at least 1 defined risk factor for MDRO.

RESULTS

During both periods, 33 (10%) and 30 (10%) among 327 and 297 admissions were, respectively, associated with a positive admission MDRO carriage. During both periods, a second screening was performed in 147 (45%) and 127 (43%) patients. Altogether, the rate of acquired MDRO (positive screening or clinical specimen) was similar during both periods (10% [n = 15] and 11.8% [n = 15], respectively; P = .66).

CONCLUSIONS

The results of our study contribute to support the safety of an isolation-targeted screening policy on ICU admission compared with universal screening and isolation regarding the rate of ICU-acquired MDRO colonization or infection.

Comparison of rates of fecal colonization with extended-spectrum beta-lactamase-producing enterobacteria among patients in different wards, outpatients and medical students

Because asymptomatic carriage of extended-spectrum beta-lactamase (ESBL) producers is a risk factor for infection, data on colonization dynamics are important when planning infection control. This study investigated fecal colonization with ESBL producers among inpatients, outpatients and medical students and compares the characteristics of ESBL producers among these groups. Carriage rates were investigated in 5581 fecal samples; 4343 from inpatients (330, 1397, 619 and 1864 from adult ICUs [intensive care units], adult non-ICUs, pediatric ICUs and pediatric non-ICUs, respectively), 814 from outpatients and 424 from screening of medical students. ESBL producers were characterized by co-resistance, integrons carried, and aminoglycoside resistance and ESBL genes. Dynamic regression models were built to identify relationships between combinations of time series of monthly antibiotic consumption, prevalence of carriers and infected subjects. Inpatients, ICU patients and adults showed higher prevalence than outpatients, non-ICU patients or children (7.4%, 9.3% and 12.0% vs. 3.1%, 6.1% and 4.1%, respectively). Klebsiella pneumoniae was more frequent in ICU patients; dominance of CTX-M-15 producers was more marked in adult than in pediatric inpatients. ESBL carriage was shown to be a consequence of infection in adults in the time-series analysis; antibiotic consumption had little effect. The epidemiology of colonization with ESBL producers differed between pediatric ICU, adult ICU and adult non-ICU patients. In adults, carriage of ESBL producers seems to be the consequence of infection, especially in ICU patients; the main source of colonization is nosocomial acquisition. In contrast, children are less likely to acquire colonizer strains in hospitals; importation of ESBL producers by colonized children seems to be significant.

Antimicrobial resistance determinants of Escherichia coli isolates recovered from some rivers in Osun State, South-Western Nigeria: Implications for public health

The inevitable development of resistance has sunk the great success achieved in the discovery of antimicrobial agents and dashed the hope of man in the recovery from infections and illnesses, as diseases and disease agents that were once thought to be controlled by antimicrobials are now re-emerging in new leagues resistance to therapy. A total of 300 PCR confirmed Escherichia coli isolates recovered from different river sources in Osun State, Nigeria were evaluated for their antibiogram profiling by the disc diffusion method and the resistant isolates were further profiled for their genotypic antimicrobial resistance determinants by polymerase chain reaction assays. Among the 20 antimicrobials selected from 10 families, resistance among sulfonamides, β-lactams and tetracyclines were found to be most frequent than phenicols and aminoglycosides with a noticeable increase in the number of multi-drug resistance ranging from three to nine antimicrobials. A total of 19 resistance determinants were assessed with their prevalence and distributions obtained as follows; [sulfonamides sulI (8%), sulII (41%)], [β-lactams; ampC 22%; blaTEM, (21%), and blaZ (18%),], [tetracyclines tetA (24%), tetB (23%), tetC (18%), tetD (78%), tetK (15%), and tetM, (10%)], [phenicols; catI (37%), catII (28%), and cmIA1 (19%)] and [aminoglycosides; aacC2 (8%), aphA1 (80%), aphA2 (80%), aadA (79%) and strA (38%)]. The Pearson chi-square exact test revealed many strong significant associations among ampC, blaTEM, blaZ and tetA genes with some determinants screened. The findings signify high increase in the prevalence of multidrug resistant E. coli isolates and resistance determinants indicating increased public health risks associated with the ingestion of waters from untreated sources. Hence, a necessity for safe water supply, provision of proper sanitation facilities and good surveillance programmes to monitor antimicrobial resistance patterns in water bodies.

Extended spectrum beta-lactamase carriage state among elderly nursing home residents in Beirut

Introduction. ESBL-producing Enterobacteriaceae can cause severe infections, but they are also isolated from the stool of asymptomatic subjects. Faecal carriage of such organism is poorly understood. Methods. First phase of the study was cross-sectional with prevalence and epidemiology of ESBL faecal carriage in two nursing homes in Beirut: 57 residents in the first (NH1) and 151 residents in the second (NH2). In second phase, faecal swabs from cohort of NH1 residents were examined for carriage at six-week intervals over three-month period. Residents' charts were reviewed to assess carriage risk factors. Results. Over 3 consecutive samplings at NH1, 81% of residents were at least one-time carriers with 50% at the first round, 60.4% at the second, and 74.5% at the last one. At NH2, 68.2% of residents were carriers. Constipation (in NH1) and antibiotic intake (in NH2) were significantly associated with higher ESBL faecal carriage while the length of stay at the nursing home (in NH2) was associated with less carriage. Conclusion. Faecal carriage of ESBL-producing Enterobacteriaceae is high among nursing home patients in Beirut. The rate of carriage changes rapidly and significantly over time either with multiple factors playing a possible role like outbreak spreading, antibiotic, and health care system exposure.

Direct RNA-based detection of CTX-M β-lactamases in human blood samples

Bloodstream infections with ESBL-producers are associated with increased mortality, which is due to delayed appropriate treatment resulting in clinical failure. Current routine diagnostics for detection of bloodstream infections consists of blood culture followed by species identification and susceptibility testing. In attempts to improve and accelerate diagnostic procedures, PCR-based methods have been developed. These methods focus on species identification covering only a limited number of ESBL coding genes. Therefore, they fail to cover the steadily further evolving genetic diversity of clinically relevant β-lactamases. We have recently designed a fast and novel RNA targeting method to detect and specify CTX-M alleles from bacterial cultures, based on an amplification-pyrosequencing approach. We further developed this assay towards a diagnostic tool for clinical use and evaluated its sensitivity and specificity when applied directly to human blood samples. An optimized protocol for mRNA isolation allows detection of specific CTX-M groups from as little as 100 CFU/mL blood via reverse transcription, amplification, and pyrosequencing directly from human EDTA blood samples as well as from pre-incubated human blood cultures with a turnaround time for test results of <7 h.

Antimicrobial susceptibility pattern of aerobic microbial isolates in a clinical laboratory in Karachi - Pakistan

Backgroun and Objective: Resistance to multiple antimicrobials is the major cause of debility and death due to infectious diseases around the world. Our objective was to determine the frequency and antimicrobial susceptibility pattern of aerobic microbial isolates in a clinical laboratory.

Methodology: All culture specimens of tissue, pus, urine, bone, blood, fluid, stool, sputum, and high vaginal swab received in the Microbiology Department of Clinical & Research Laboratory, Baqai Institute of Diabetology and Endocrinology from May 2010 to January 2011 were included in the present study. Bacterial isolates were identified and their antimicrobial susceptibility pattern was determined.

Results: Out of 312 cultured specimens, 272 (87.17%) were found infected with 437 microbial organisms (412 bacteria and 25 Candida isolates). A total of 90 (20.59%) multi-drug resistant (MDR) isolates were found. MDR Escherichia coli was isolated in 40 (34.19%) out of 117 culture specimens which showed the growth of Escherichia coli, Pseudomonas aeruginosa in 17 (22.08%), Methicillin-resistant Staphylococcus aureus in 13 (11.50%), Klebsiella pneumoniae in 7 (22.58%), Proteus species in 6 (31.58%), Acinetobacter species in 3 (33.33%), Enterobacter species in 2 (28.57%), Coliform (Escherichia coli) in 1 (16.67%) and Enterococcus species were isolated in 1 (50%) culture specimen.

Conclusions: High prevalence of multi-drug resistant bacteria was found in the present study. Emergence of antimicrobial resistance has become a major challenge in infectious disease medicine. Antimicrobial resistance may be due to misuse of antimicrobials by physicians and self medication in Pakistan. Further large scale studies are needed to validate our findings.

A survey of drug resistance bla genes originating from synthetic plasmid vectors in six Chinese rivers

Antibiotic resistance poses a significant challenge to human health and its rate continues to rise globally. While antibiotic-selectable synthetic plasmid vectors have proved invaluable tools of genetic engineering, this class of artificial recombinant DNA sequences with high expression of antibiotic resistance genes presents an unknown risk beyond the laboratory setting. Contamination of environmental microbes with synthetic plasmid vector-sourced antibiotic resistance genes may represent a yet unrecognized source of antibiotic resistance. In this study, PCR and real-time quantitative PCR were used to investigate the synthetic plasmid vector-originated ampicillin resistance gene, β-lactam antibiotic (blá), in microbes from six Chinese rivers with significant human interactions. Various levels of blá were detected in all six rivers, with the highest levels in the Pearl and Haihe rivers. To validate the blá pollution, environmental plasmids in the river samples were captured by the E. coli transformants from the community plasmid metagenome. The resultant plasmid library of 205 ampicillin-resistant E. coli (transformants) showed a blá-positive rate of 27.3% by PCR. Sequencing results confirmed the synthetic plasmid vector sources. In addition, results of the Kirby-Bauer disc-diffusion test reinforced the ampicillin-resistant functions of the environmental plasmids. The resistance spectrum of transformants from the Pearl and Haihe rivers, in particular, had expanded to the third- and fourth-generation of cephalosporin drugs, while that of other transformants mainly involved first- and second-generation cephalosporins. This study not only reveals environmental contamination of synthetic plasmid vector-sourced blá drug resistance genes in Chinese rivers, but also suggests that synthetic plasmid vectors may represent a source of antibiotic resistance in humans.

Outbreak of extended spectrum beta-lactamase-producing Klebsiella pneumoniae in an intensive care unit (Brest)

INTRODUCTION

We had for aim to describe control and investigation of an outbreak caused by a strain of Extended spectrum beta-lactamase producing Klebsiella pneumoniae in intensive care units of the Brest teaching hospital.

PATIENTS AND METHOD

The case definition was a patient infected by or carrying the epidemic strain. Control measures and investigations are presented. A case-control study was conducted in the surgical intensive care unit. Each case was matched with two controls based on admission times in the unit. The study focused on diagnostic and therapeutic procedures, and potential contacts with healthcare workers, in this context of cross transmission.

RESULTS

Between February and May 2011, nine cases were reported in the surgical ICU and two in the medical ICU. Eighteen controls were matched with the nine surgical ICU cases. Several factors were found to be statistically associated with infection or colonization by the epidemic strain: the surgical block in which patients had been operated and the ward of first hospitalization; the number of trans-esophageal and trans-thoracic echocardiographies, of central venous catheter insertions, and of surgical operations; intubation. The total number of invasive procedures was also found to be statistically higher among cases.

CONCLUSION

This study identified factors associated with colonization or infection by the epidemic strain. These factors might have been involved in the transmission tree, and be vulnerable elements for the prevention of nosocomial infections and colonisations, and their epidemic spread.

Impact of ceftriaxone de-restriction on the occurrence of ESBL-positive bacterial strains and antibiotic consumption

As a cost-saving measure, the Drug and Therapeutics Committee (DTC) removed ceftriaxone from the list of restricted antibiotics in May, 2008, which permitted its use as a first-line antibiotic. To evaluate the impact of this change, the occurrence of extended-spectrum beta-lactamase (ESBL)-positive bacterial strains and antibiotic consumption were monitored for 2 years before and after the intervention. In the post-intervention period, ceftriaxone utilization increased, while total antibiotic utilization did not change significantly. The utilization of all restricted antibiotics decreased (p <0.05) in the post-intervention period. Utilization of carbapenems increased (p <0.05), while utilization of quinolones increased nonsignificantly. The density of resistant ESBLs increased (p = 0.001) from 0.99 to 1.34 per 1000 bed-days from the pre- to the postintervention period. Ceftriaxone use was significantly correlated with ESBL occurrence (p <0.005). It can be concluded that ceftriaxone de-restriction increased the occurrence of ESBLs and the utilization of carbapemens.

The revolving door between hospital and community: extended-spectrum beta-lactamase-producing Escherichia coli in Dublin

BACKGROUND

Escherichia coli that produce extended-spectrum beta-lactamases (ESBLs) are an increasing cause of healthcare-associated infection, and community healthcare facilities may be a reservoir for important epidemic clones.

AIM

To characterize retrospectively and investigate the epidemiology of ESBL-producing E. coli collected in a Dublin hospital, during 2009 and 2010, and to investigate the dissemination of specific clones within hospital and community healthcare facilities.

METHODS

Pulsed-field gel electrophoresis (PFGE) was used to determine the genetic relatedness of 100 ESBL-producing E. coli isolates. Phylogenetic groups were determined and the O25b-ST131 clone identified in the collection. The genetic data were correlated with antimicrobial susceptibility, clinical and demographic data to explore the epidemiology of specific clones.

FINDINGS

Phylogenetic groups B2 (62%) and D (18%) were the most common and were associated with non-urinary isolates (P<0.0001 by Fisher's exact test). PFGE revealed 12 clusters (≥ 80% similarity), the largest of which clustered with the epidemic UK strain A. Residents of long-term care facilities (LTCFs) in the community exclusively carried the O25b-ST131 clone and phylogenetic groups B2 and D.

CONCLUSIONS

E. coli O25b-ST131 is largely responsible for ESBL-producing E. coli in LTCFs in Dublin. The distribution of ESBL-producing E. coli in our hospital and community highlights a 'revolving door' through which these resistant bacteria spread and disseminate.

Patient's origin and lifestyle associated with CTX-M-producing Escherichia coli: a case-control-control study

Background

Global dissemination of Escherichia coli producing CTX-M extended-spectrum β-lactamases (ESBL) is a public health concern. The aim of the study was to determine factors associated with CTX-M- producing E. coli infections among patients hospitalised in the Assistance Publique-Hôpitaux de Paris, the largest hospital system in France (23 000 beds), through a prospective case-control-control study.

Methods/Principal Findings

From November 2008 to June 2009, 152 inpatients with a clinical sample positive for CTX-M-producing E. coli (cases), 152 inpatients with a clinical sample positive for non ESBL-producing E. coli on the day or within the three days following case detection (controls C1), and 152 inpatients with culture-negative clinical samples since the beginning of hospitalisation and until three days after case detection (controls C2) were included in ten hospitals of the Paris area. Factors studied were related to patient's origin, lifestyle and medical history as well as care during hospitalisation. Those independently associated with CTX-M-producing E. coli were determined. Three independent factors were common to the two case-control comparisons: birth outside of Europe (cases vs C1: OR₁ = 2.4; 95%CI = [1.3–4.5] and cases vs C2: OR₂ = 3.1; 95%CI = [1.4–7.0]), chronic infections (OR₁ = 2.9; 95%CI = [1.3–6.9] and OR₂ = 8.7; 95%CI = [2.0–39.7]), and antibiotic treatment between hospital admission and inclusion (OR₁ = 2.0; 95%CI = [1.0–3.8] and OR₂ = 3.3; 95%CI = [1.5–7.2]). Cases were also more likely to be (i) functionally dependent before hospitalisation than C2 (OR₂ = 7.0; 95%CI = [2.1–23.5]) and (ii) living in collective housing before hospitalisation than C2 (OR₂ = 15.2; 95%CI = [1.8–130.7]) when CTX-M-producing E. coli was present at admission.

Conclusion

For the first time, patient's origin and lifestyle were demonstrated to be independently associated with isolation of CTX-M-producing E. coli, in addition to health care-related factors.