Estimating the association between antibiotic exposure and colonization with extended-spectrum ß-lactamase-producing Gram-negative bacteria using machine learning methods: a multicentre, prospective cohort study.

OBJECTIVES: The aim of the study was to measure the impact of antibiotic exposure on the acquisition of colonization with extended-spectrum ß-lactamase-producing Gram-negative bacteria (ESBL-GNB) accounting for individual- and group-level confounding using machine-learning methods. METHODS: Patients hospitalized between September 2010 and June 2013 at six medical and six surgical wards in Italy, Serbia and Romania were screened for ESBL-GNB at hospital admission, discharge, antibiotic start, and after 3, 7, 15 and 30 days. Primary outcomes were the incidence rate and predictive factors of new ESBL-GNB colonization. Random forest algorithm was used to rank antibiotics according to the risk of selection of ESBL-GNB colonization in patients not colonized before starting antibiotics. RESULTS: We screened 10 034 patients collecting 28 322 rectal swab samples. New ESBL-GNB colonization incidence with and without antibiotic treatment was 22/1000 and 9/1000 exposure-days, respectively. In the adjusted regression analyses, antibiotic exposure (hazard ratio (HR) 2.38; 95% CI 1.29-4.40), age 60-69 years (HR 1.19; 95% CI 1.05-1.34), and spring season (HR 1.25; 95% CI 1.14-1.38) were independently associated with new colonization. Monotherapy ranked higher als combination therapy in promoting ESBL-GNB colonization. Among monotherapy, cephalosporins ranked first followed by tetracycline (second), macrolide (fourth) and cotrimoxazole (seventh). Overall the ranking of cephalosporins was lower when used in combination. Among combinations not including cephalosporins, quinolones plus carbapenems ranked highest (eighth). Among sequential therapies, quinolones ranked highest (tenth) when prescribed within 30 days of therapy with cephalosporins. CONCLUSIONS: Impact of antibiotics on selecting ESBL-GNB at intestinal level varies if used in monotherapy or combination and according to previous antibiotic exposure. These finding should be explored in future clinical trials on antibiotic stewardship interventions. CLINICAL TRIAL REGISTRATION: NCT01208519.

High rates of intestinal colonisation with fluoroquinolone-resistant ESBL-harbouring Enterobacteriaceae in hospitalised patients with antibiotic-associated diarrhoea.

The purposes of this study were to investigate the intestinal carriage of extended-spectrum ß-lactamase-harbouring Enterobacteriaceae (ESBL-EN) and associated fluoroquinolone resistance (FQ-R) in 120 hospitalised patients with antibiotic-associated diarrhoea, and to investigate a correlation between Clostridium difficile (C. difficile) infection and intestinal colonisation with ESBL-EN in these patients. Stool samples were screened for C. difficile infection by toxin A/B enzyme-linked immunosorbent assay (ELISA) and for the presence of enterobacterial isolates producing ß-lactamases by plating on ß-lactamase screening (BLSE) agar. Recovered isolates were confirmed pheno- and genotypically for the presence of ESBL genes (bla CTX-M, bla TEM, bla SHV) by the double-disc synergy test and polymerase chain reaction (PCR) sequencing, and tested for the presence of topoisomerase mutations (gyrA, parC) and plasmid-mediated quinolone resistance (PMQR) determinants [qnrA, qnrB, qnrS, qepA, aac(6')-Ib-cr] by PCR sequencing. ESBL-EN were detected in 44/120 (37 %) stool samples. C. difficile-infected patients showed a significantly higher frequency of intestinal colonisation with ESBL-EN compared to C. difficile non-infected patients (62 % vs. 31 %, p = 0.008). Of the 73 ESBL-EN recovered, 46 (63 %) showed high-level FQ-R [ciprofloxacin minimum inhibitory concentration (MIC) ≥32 mg/L]. The largest group consisted of 21 bla CTX-M-15-harbouring Enterobacteriaceae (ciprofloxacin MIC ≥64 mg/L) with multiple topoisomerase mutations in gyrA and parC, in combination with co-carriage of aac(6')-Ib-cr. Most of them were Escherichia coli isolates belonging to sequence types ST131 and ST410. We found remarkably high rates of intestinal colonisation with high-level FQ-R ESBL-EN in hospitalised patients with antibiotic-associated diarrhoea, especially among C. difficile-infected patients. These data underscore the need for stringent infection control to contain this potentially infectious and multidrug-resistant reservoir.

Risk factors for colonization with extended-spectrum beta-lactamase-producing enterobacteriaceae on admission to rehabilitation centres.

Patients newly admitted to rehabilitation centres are at high risk of colonization with multidrug-resistant bacteria because many of them have experienced prolonged stays in other healthcare settings and have had high exposure to antibiotics. We conducted a prospective study to determine the prevalence of and risk factors for colonization with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) in this population. Subjects were screened by rectal swab for ESBL-PE within 2 days of admission. Swabs were plated on chromagar ESBL plates and the presence of ESBL was verified by a central laboratory. A multilevel mixed effects model was used to identify risk factors for ESBL-PE colonization. Of 2873 patients screened, 748 (26.0%) were positive for ESBL-PE. The variables identified as independently associated with ESBL-PE colonization were: recent stay in an acute-care hospital for over 2 weeks (OR=1.34; 95% CI, 1.12, 1.6), history of colonization with ESBL-PE (OR=2.97; 95% CI, 1.99, 4.43), unconsciousness on admission (OR=2.59; 95% CI, 1.55, 4.34), surgery or invasive procedure in the past year (OR=1.49; 95% CI, 1.2, 1.86) and antibiotic treatment in the past month (OR=1.80; 95% CI, 1.45, 2.22). The predictive accuracy of the model was low (area under the ROC curve 0.656). These results indicate that ESBL-PE colonization is common upon admission to rehabilitation centres. Some risk factors for ESBL-PE colonization are similar to those described previously; however, newly identified factors may be specific to rehabilitation populations. The high prevalence and low ability to stratify by risk factors may guide infection control and empirical treatment strategies in rehabilitation settings.

Comparative population analysis of Klebsiella pneumoniae strains with extended-spectrum ß-lactamases colonizing patients in rehabilitation centers in four countries.

The international project MOSAR was conducted in five rehabilitation centers; patients were screened for rectal carriage of extended-spectrum ß-lactamase (ESBL)-producing members of the Enterobacteriaceae. Among 229 Klebsiella pneumoniae isolates, four clonal groups (CG) or complexes (CC) prevailed: CG17 in France, CG101 in Italy, CG15 in Spain, and CC147 in Israel. ESBLs, mainly CTX-Ms, were produced by 226 isolates; three isolates expressed AmpC-like cephalosporinases. High genetic diversity of K. pneumoniae populations was observed, with specific characteristics at each center.

Asymptomatic rectal carriage of blaKPC producing carbapenem-resistant Enterobacteriaceae: who is prone to become clinically infected?

Carbapenem-resistant Enterobacteriaceae (CRE) are emerging extremely drug-resistant pathogens; blaKPC is the predominant carbapenemase in Israel. Early detection of asymptomatic rectal carriers is important for infection control purposes. We aimed to determine who among newly identified CRE rectal carriers is prone to have a subsequent clinical specimen with CRE. A matched case-control study was conducted in a tertiary care teaching hospital in Israel. Cases with a primary positive CRE rectal test and subsequent CRE clinical specimens were matched in a 1:2 ratio with CRE rectal carriers who did not develop subsequent CRE clinical specimens (controls). Matching was based on calendar time of primary CRE isolation, whether the primary CRE isolation was ≤ 48 h or > 48 h after hospital admission, and time at risk to have a subsequent clinical specimen. Data were extracted from the patients' medical records and from the hospital's computerized database. One hundred and thirty-two newly identified CRE rectal carriers (44 cases, 88 controls) were included. The median time interval between screening and subsequent clinical specimens was 11 days (range, 3-27); 86% of the clinical specimens were classified as true infections. Independent predictors of subsequent CRE clinical specimens were: admission to the intensive care unit, having a central venous catheter, receipt of antibiotics, and diabetes mellitus. Identification of the risk factors for subsequent infections among CRE-colonized patients can be used to control modifiable risk factors and to direct empirical antimicrobial therapy when necessary.

Clonal structure, extended-spectrum ß-lactamases, and acquired AmpC-type cephalosporinases of Escherichia coli populations colonizing patients in rehabilitation centers in four countries.

The prospective project MOSAR was conducted in five rehabilitation units: the Berck Maritime Hôpital (Berck, France), Fondazione Santa Lucia (Rome, Italy), Guttmann Institute (GI; Barcelona, Spain), and Loewenstein Hospital and Tel-Aviv Souraski Medical Center (TA) (Tel-Aviv, Israel). Patients were screened for carriage of Enterobacteriaceae resistant to expanded-spectrum cephalosporins (ESCs) from admission until discharge. The aim of this study was to characterize the clonal structure, extended-spectrum ß-lactamases (ESBLs), and acquired AmpC-like cephalosporinases in the Escherichia coli populations collected. A total of 376 isolates were randomly selected. The overall number of sequence types (STs) was 76, including 7 STs that grouped at least 10 isolates from at least three centers each, namely, STs 10, 38, 69, 131, 405, 410, and 648. These clones comprised 65.2% of all isolates, and ST131 alone comprised 41.2%. Of 54 STs observed only in one center, some STs played a locally significant role, like ST156 and ST393 in GI or ST372 and ST398 in TA. Among 16 new STs, five arose from evolution within the ST10 and ST131 clonal complexes. ESBLs and AmpCs accounted for 94.7% and 5.6% of the ESC-hydrolyzing ß-lactamases, respectively, being dominated by the CTX-M-like enzymes (79.9%), followed by the SHV (13.5%) and CMY-2 (5.3%) types. CTX-M-15 was the most prevalent ß-lactamase overall (40.6%); other ubiquitous enzymes were CTX-M-14 and CMY-2. Almost none of the common clones correlated strictly with one ß-lactamase; although 58.7% of ST131 isolates produced CTX-M-15, the clone also expressed nine other enzymes. A number of clone variants with specific pulsed-field gel electrophoresis and ESBL types were spread in some locales, potentially representing newly emerging E. coli epidemic strains.

Transmission dynamics of ESBL-producing Escherichia coli clones in rehabilitation wards at a tertiary care centre.

Increasing resistance due to the production of ESBL in Escherichia coli (ESBL-E. coli) has become a major threat to public health. Our aims were to study the incidence of ESBL-E. coli acquisition during hospitalization and the transmission rates of different ESBL-E. coli clones. This was a prospective case-control study, conducted in two geriatric rehabilitation wards in Tel-Aviv. Serial rectal cultures were collected from admission till discharge. All patient-unique ESBL-E. coli isolates were subjected to molecular typing by PFGE, MLST and determination of ESBL genes. An acquisition of ESBL-E. coli was defined as traceable when a patient with the same ST, PFGE type and ESBL gene was hospitalized in the same ward in parallel to the acquisition case. ESBL-E. colis were recovered from 125 patients out of 492 enrolled: 52 were recovered upon admission, 59 acquired ESBL-E. coli during their stay, and there was undetermined status in 14 patients. A low Norton's score was associated with acquisition (O.R. 1.14 for each point, 95% C.I. 1.01-1.29, p < 0.05). ESBL-E. coli infections (n = 9) had occurred only in ESBL-E. coli carriers. The pandemic ST131 clone was the most common (48/125). The majority of the isolates (101/125) produced CTX-M-type ESBL. Of the 59 acquisition cases, 32 were traced to another patient. In-hospital dissemination was highest in the CTX-M-27-producing ST131 and the SHV-5-producing ST372 sub-clones (acquisition/admission ratios of 17/11 and 9/3, respectively), with almost all cases traced to other patients. In conclusion, most ESBL-E. coli acquisition cases were traceable to other patients. The transmission potential varied significantly between ESBL-E. coli clones.

Carriage of methicillin-resistant Staphylococcus aureus on admission to European rehabilitation centres--a prospective study.

This study aimed to determine the prevalence of and risk factors for methicillin-resistant Staphylococcus aureus (MRSA) carriage among patients newly admitted to rehabilitation centres. It is a prospective study examining MRSA carriage on admission to seven rehabilitation wards in four countries. Risk factors for MRSA carriage were analysed using univariate and multivariate analyses. A total of 1204 patients were studied. Among them, 105 (8.7%) had a positive admission MRSA screening result. The MRSA carriers were more likely to be male, to have had a recent stay in another long-term-care facility or >2 weeks acute-care hospital stay, history of colonization with MRSA, reduced level of consciousness, peripheral vascular disease and pressure sores. In multivariable logistic regression male gender (odds ratio (OR) 2.2, 95% confidence interval (CI) 1.4-3.6, p 0.001), history of MRSA positivity (OR 6.8, 95% CI 3.8-12.3, p <0.001), peripheral vascular disease (OR 2.5, 95% CI 1.2-5, p 0.013), recent stay in another long-term-care facility (OR 2.1, 95% CI 1.3-3.5, p 0.004), or long (>2 weeks) acute-care hospital stay (OR 1.9, 95% CI 1.2-3, p 0.004), remained significant risk factors for MRSA carriage. MRSA carriage is common on admission to rehabilitation centres but less so, than previously described in long-term-care facilities. Male gender, history of MRSA positivity, previous hospitalization and peripheral vascular disease may predict MRSA carriage, and may serve as indicators for using pre-emptive infection control measures.

Culture-based detection of methicillin-resistant Staphylococcus aureus by a network of European laboratories: an external quality assessment study.

Twenty-three hospital laboratories from Europe and Israel participated in an external quality assessment (EQA) of the culture-based detection of methicillin-resistant Staphylococcus aureus (MRSA). Participants also reported the MRSA prevalence in clinical cultures and patient screening specimens, as well as the MRSA screening practices employed at their hospitals. An EQA panel of 18 samples consisting of two MRSA harbouring SCCmec IV and I, and one strain each of methicillin-resistant coagulase-negative S. epidermidis, methicillin-sensitive S. aureus and Escherichia coli as pure strains or in mixtures at 10(7)-1 cfu absolute loads was analysed by the 23 participants. Seventeen (74%) participants identified 17 or more samples correctly. Of these, 15 (88%) utilised a chromogenic medium alone (ChromID, bioMérieux; BBL CHROMagar, BD Diagnostics; MRSA Select, Bio-Rad Laboratories) or combined with a conventional medium and up to three confirmatory tests. Proportions of MRSA among S. aureus isolated from clinical cultures varied widely, even among hospitals within countries, ranging from 11-20% to 61-70%. MRSA carriage rates were less variable (0-20%) between countries. Almost all participants (n=22, 96%) screened patients for MRSA carriage during 2009-2010, of which 15 (68%) screened intensive care unit (ICU) patients alone or combined with other targeted high-risk groups, and 10 (45%) combined nasal screening with another body site.