Marlène Sauget

The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify bla_ESBL and bla_AmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one bla_ESBL or bla_AmpC, with bla_CTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). bla_CMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with bla_CMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. bla_CTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which bla_CMY-2 dominated through two dominant serovars in this collection.

The worldwide spread of Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL-Kp) is a significant threat. Specifically, various pandemic clones of ESBL-Kp are involved in hospital outbreaks and caused serious infections. In that context, we assessed the phenotypic and molecular features of a collection of ESBL-Kp isolates in a French university hospital and evaluated the occurrence of potential cross-transmissions. Over a 2-year period (2017–2018), 204 non-duplicate isolates of ESBL-Kp were isolated from clinical (n = 118, 57.8%) or screening (n = 86, 42.2%) sample cultures. These isolates were predominantly resistant to cotrimoxazole (88.8%) and ofloxacin (82.8%) but remained susceptible to imipenem (99.3%) and amikacin (93.8%). CTX-M-15 was the most frequent ESBL identified (83.6%). Multilocus sequence typing and pulse-field gel electrophoresis analysis showed an important genetic variability with 41 sequence types (ST) and 50 pulsotypes identified, and the over representation of the international epidemic clones ST307 and ST405. An epidemiological link attesting probable cross-transmission has been identified for 16 patients clustered in 4 groups during the study period. In conclusion, we showed here the dissemination of pandemic clones of ESBL-Kp in our hospital on a background of clonal diversity.

The worldwide spread of E. coli ST131 has significantly contributed to the dissemination of E. coli producing extended-spectrum β-lactamases (ESBL). In a French University hospital, we assessed the molecular features of ESBL-producing E. coli and identified risk factors in patients for colonization or infection with E. coli ST131. Over a 2-year period (2015–2017), each patient with at least one clinical isolate or one screening isolate positive with ESBL-producing E. coli were included (n = 491). The ST131 clonal group accounted for 17.5% (n = 86) of all ESBL-producing E. coli and represented 57.3% isolates of phylogroup B2. FimH-based sub-typing showed that 79.1% (68/86) of ST131 isolates were fimH30, among which 67.6% (n = 46), 20.6% (n = 14) and 11.8% (n = 8) isolates harbored genes encoding the ESBL CTX-M-15, CTX-M-27, and CTX-M-14, respectively. The multivariate analysis identified two factors independently associated with ST131 ESBL-producing E. coli isolates: infection (Odds ratio [OR] = 1.887, 95% confidence interval [CI]: 1.143–3.115; p = 0.013) and community acquisition (OR = 2.220, 95% CI: 1.335–3.693; p = 0.002). In conclusion, our study confirmed the predominance of ST131 clonal group among ESBL-producing E. coli and the difficulty to identify common risk factors associated with carriage of this pandemic clonal group.

The epidemiology of Staphylococcus aureus is changing and several surveillances worldwide have evidenced an increasing incidence of S. aureus bloodstream infections (BSIs). Here, we described the long-term epidemiology of the emergent clonal group CC398 among S. aureus isolated from BSIs in our French university hospital between 2010 and 2017. Each patient with at least one blood culture positive with S. aureus during the study period was included (N = 1455). Cefoxitin susceptibility was determined using the disk diffusion method according to EUCAST recommendations. CC398 isolates were first screened from the whole S. aureus collection with a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) typing method confirmed by a CC398-specific PCR. In our hospital, the incidence of hospital- and community-acquired BSIs due to S. aureus and MSSA increased in parallel between 2010 and 2017 while that of BSIs with MRSA decreased. The prevalence of CC398 isolates among S. aureus from BSIs increased from 3.6 in 2010 to 20.2% in 2017 (p < 0.05). CC398-MRSA emerged but remains very sparse. Our data suggested that CC398-MSSA disseminates in the community. We showed here the emergence and the diffusion of CC398-MSSA, a subclone associated with invasive infections, in our hospital. The monitoring of this particular human-adapted S. aureus clone is needed and genomic studies will have to identify the determinants of its diffusion.

Introduction: Pseudomonas aeruginosa is one of the most common nosocomial pathogens, known with a wide resistance to antimicrobials. Carbapenemases producing Pseudomonas aeruginosa is a growing global public health concern as this pathogen is easily transmissible among patients. Metallo-Beta-lactamases is the most important class of these carbapenemases with their broad-spectrum resistance profile. This study was conducted to investigate the prevalence of MBL-producing P. aeruginosa collected in an Algerian hospital. Methodology: All Metallo-β-lactamase (MBL)-producing P. aeruginosa isolates recovered from patients during a 2 years period (2015-2016) were studied using a combination of phenotypic and molecular typing methods (susceptibility testing, molecular characterization of carbapenemase-encoding genes, multi-locus sequence typing and pulsed-field gel electrophoresis). Results: A total of twenty-six MBL producing P. aeruginosa of 188 isolates were investigated. The burns unit ranked in the first position of the majority of identified cases with 73.07%. About 73.07% of total MBL isolates were mainly isolated from pus samples. The studied isolates were subjected to the molecular typing, in which 4 different Dra1-PFGE patterns and 3 sequences type were assigned (ST244, ST381, and ST1076), and all isolates were revealed positive for VIM-4. Conclusions: We report the third description of blaVIM-4 in Algeria indicating the emergence and spread of carbapenemase-encoding genes among P. aeruginosa in the hospital environment.

Antibiotic resistance is a major public health problem requiring the early optimization of antibiotic prescriptions. Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS) has been shown to accurately identify bacteria from positive blood culture. Here, we developed a rapid detection of Escherichia coli resistance to amoxicillin (AMX) and cefotaxime (CTX) from positive blood culture based on MALDI-TOF MS. Potential sparing of broad-spectrum antibiotics was also evaluated. We tested 103 E. coli-positive blood cultures. Blood cultures were subculture 1-hour in antibiotic-free rich liquid media before further incubation with and without AMX for 2.5 h or CTX for 2 h. Protein extracts associated with an internal control were spotted on a MALDI-TOF target and spectra were analyzed with the MBT-ASTRA prototype software (Bruker Daltonik GmbH, Bremen, Germany). Bacterial growth ratio was calculated from the AUC spectra obtained in the presence and absence of the antibiotic and compared to a threshold which classified E. coli as susceptible or resistant. Results were interpreted with MICs determined using agar dilution method as reference technique. MBT-ASTRA recognized 95% and 84% of the AMX- and CTX-susceptible isolates, respectively. Overall, quantitative analysis of mass spectra allows susceptibility testing within 4 hours after the positivity of blood culture with E. coli. At the first report of positive blood culture, MALDI-TOF MS would then provide the prescribers with the bacterial identification and the susceptibility to AMX and CTX, thus limiting the use of broad-spectrum compounds.