Erwinia billingiae as Unusual Cause of Septic Arthritis, France, 2017.

In 2017 in France, we treated a patient with knee septic arthritis caused by Erwinia billingiae after trauma involving a palm tree. This rare pathogen could only be identified through 16S rRNA gene sequencing. For bacterial infections after injuries with plants, 16S rRNA gene sequencing might be required for species identification.

Multicenter Study of Cronobacter sakazakii Infections in Humans, Europe, 2017.

Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. sakazakii isolates collected during 2017 to a study center in Austria. Testing at the center included species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, subtyping by whole-genome sequencing (WGS), and determination of antimicrobial resistance. Eleven countries sent 77 isolates, including 36 isolates from 2017 and 41 historical isolates. Fifty-nine isolates were confirmed as C. sakazakii by WGS, highlighting the challenge of correctly identifying Cronobacter spp. WGS-based typing revealed high strain diversity, indicating absence of multinational outbreaks in 2017, but identified 4 previously unpublished historical outbreaks. WGS is the recommended method for accurate identification, typing, and detection of this pathogen.

Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014.

We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-ß-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.

Carbapenem-Resistant Enterobacter cloacae in Patients from the US Veterans Health Administration, 2006-2015.

We analyzed carbapenem-resistant Enterobacteriaceae (CRE) trends among patients from the US Veterans Health Administration (VHA). After the emergence of CRE in the eastern United States, resistance rates remained stable in Klebsiella pneumoniae but increased in Enterobacter cloacae complex, suggesting a "second epidemic". VHA offers a vantage point for monitoring nationwide CRE trends.

Emergence of blaNDM-7-Producing Enterobacteriaceae in Gabon, 2016.

Reports of carbapenemase-producing Enterobacteriaceae in Africa remain rare and assess mostly blaOXA-48-producing isolates from Mediterranean countries and South Africa. We identified blaNDM-7-producing Enterobacteriaceae in Gabon in 2016. The isolates contained blaNDM-7 IncX3 plasmids that were unusual and similar to the one described in a colistin-resistant Klebsiella pneumoniae SZ04 isolate from China.

Australian Group on Antimicrobial Resistance Australian Enterobacteriaceae Sepsis Outcome Programme annual report, 2014.

The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2014 survey was the second year to focus on blood stream infections. During 2014, 5,798 Enterobacteriaceae species isolates were tested using commercial automated methods (Vitek 2, BioMérieux; Phoenix, BD) and results were analysed using the Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2015). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 9.0%/9.0% of Escherichia coli (CLSI/EUCAST criteria) and 7.8%/7.8% of Klebsiella pneumoniae, and 8.0%/8.0% K. oxytoca. Non-susceptibility rates to ciprofloxacin were 10.4%/11.6% for E. coli, 5.0%/7.7% for K. pneumoniae, 0.4%/0.4% for K. oxytoca, and 3.5%/6.5% in Enterobacter cloacae. Resistance rates to piperacillin-tazobactam were 3.2%/6.8%, 4.8%/7.2%, 11.1%/11.5%, and 19.0%/24.7% for the same 4 species respectively. Fourteen isolates were shown to harbour a carbapenemase gene, 7 blaIMP-4, 3 blaKPC-2, 3 blaVIM-1, 1 blaNDM-4, and 1 blaOXA-181-lke.

Detection and epidemiology of carbapenemase producing Enterobacteriaceae in the Netherlands in 2013-2014.

Laboratory detection of carbapenemase-producing Enterobacteriaceae (CPE) is complicated. Screening with MIC values below clinical breakpoints followed by genotypic confirmation is recommended. We evaluated the application of recommended CPE screening and confirmation methods and provide an overview of CPE epidemiology in E. coli and K. pneumoniae in the Netherlands. Data on E. coli and K. pneumoniae isolates with elevated meropenem (>0.25 mg/L) and/or imipenem (>1 mg/L) MIC values in 2013-2014 were selected from the Infectious Disease Surveillance Information System for Antibiotic Resistance. Laboratories were requested to provide additional results of any confirmatory testing performed. Confirmation of elevated carbapenem MIC values using gradient testing was performed in 59.8 % of eligible isolates. Confirmatory testing showed elevated MIC values in 8 % of E. coli and 32 % of K. pneumoniae isolates. The overall proportion of confirmed non-susceptible E. coli and K. pneumoniae was 0.01 % and 0.16 %, respectively. Genotypic confirmation was performed in 61.0 % of isolates with confirmed elevated carbapenem MIC values. A carbapenemase gene was identified in 47 % of E. coli and 65 % of K. pneumoniae isolates. OXA-48, NDM and KPC were the most frequently found carbapenemase genes. The majority (62 %) of CPE isolates was detected through targeted screening. CPE are a rare finding in the Netherlands. Adherence to the national guideline is suboptimal and differs between laboratories, implying a risk of inadequate CPE detection. Since accurate identification of CPE is the first step in prevention of CPE spread, successful implementation of guidelines for testing and reporting of CPE is essential.

Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit.

BACKGROUND: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. METHODS: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. RESULTS: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. CONCLUSION: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates.

Carbapenemase and virulence factors of Enterobacteriaceae in North Lebanon between 2008 and 2012: evolution via endemic spread of OXA-48.

OBJECTIVES: To investigate the resistance to carbapenems in Enterobacteriaceae and the underlying resistance mechanisms in North Lebanon between 2008 and 2012. METHODS: A total of 2767 Enterobacteriaceae isolates recovered from clinical samples collected in Nini Hospital (North Lebanon) were screened for a decrease in susceptibility or resistance to ertapenem (MIC >0.25 mg/L). Enterobacteriaceae were similarly screened from 183 faecal samples obtained from non-hospitalized patients. The bacterial isolates were assigned to clonal lineages by PFGE and multilocus sequence typing. Carbapenemase genes, their genetic environment and virulence genes were characterized by molecular approaches. RESULTS: The rate of Enterobacteriaceae exhibiting a decrease in susceptibility or resistance to ertapenem increased from 0.4% in 2008-10 to 1.6% in 2012 for the clinical isolates recovered from hospitalized patients. Of these isolates, scattered among seven enterobacterial species, 88% produced OXA-48 carbapenemase. However, Escherichia coli represented 73% of the OXA-48-producing Enterobacteriaceae collected in 2012 at this hospital. During the faecal carriage study performed in non-hospitalized patients, E. coli was the only species producing OXA-48. The bla(OXA-48) gene was mainly found within Tn1999.2-type transposons inserted into E. coli chromosomes or in ∼50, ∼62 or ∼85 kb plasmids. The plasmids and chromosomal inserts were related to pOXA-48a. Molecular typing of the isolates revealed clonal diversity of E. coli and Klebsiella pneumoniae producing OXA-48. OXA-48 was observed in all major E. coli phylogroups, including D and B2, and isolates harbouring virulence genes of extra-intestinal pathogenic E. coli. Although not belonging to highly virulent capsular genotypes, the OXA-48-producing K. pneumoniae harboured genes associated with virulence or host colonization. CONCLUSIONS: Horizontal transfer of related plasmids has facilitated the spread of the bla(OXA-48) gene into several Enterobacteriaceae species, including virulent E. coli. Their clonal diversity and the presence of faecal carriers in the community suggest an endemic spread of OXA-48.

Incidence rates of carbapenemase-producing Enterobacteriaceae clinical isolates in France: a prospective nationwide study in 2011-12.

OBJECTIVES: To determine proportions and incidence rates of Enterobacteriaceae producing carbapenemase among those non-susceptible (NS) to carbapenems in France. METHODS: From November 2011 to April 2012, 71 laboratories recorded non-duplicate Enterobacteriaceae clinical isolates NS to at least one carbapenem and the total number of isolates of the different species. Carbapenem MICs were determined by broth microdilution and the ß-lactamase content by DNA microarray. RESULTS: During the study period, the 71 laboratories identified 133 244 Enterobacteriaceae isolates, of which 846 (0.63%) were NS to at least one carbapenem. Carbapenem-NS isolates accounted for 0.07% (61/90 148) among Escherichia coli isolates, 1.1% (111/10 436) among Klebsiella pneumoniae, 8.2% (492/5971) among Enterobacter cloacae and 4.0% (84/2104) among Enterobacter aerogenes. Among the 541 available carbapenem-NS isolates, 222 (including 63 randomly selected E. cloacae) were further analysed after confirmation of carbapenem non-susceptibility. None of the Enterobacter spp. isolates produced carbapenemase. Among the other species, 28 isolates produced carbapenemases (22 OXA-48, 4 KPC and 2 NDM), accounting for an estimated proportion of carbapenemase-producing isolates of 0.08% for all species, 0.01% for E. coli and 0.27% for K. pneumoniae. The incidence-density rate in the participating hospitals was 0.0041 per 1000 hospital-days and the incidence rate was 0.0027 per 100 admissions. CONCLUSIONS: The incidence-density rate of carbapenemase-producing isolates per 1000 hospital-days was low and 30-fold lower than that of carbapenem-NS isolates (0.125) and almost 300-fold lower than that of ESBL-producing isolates (1.104) in these French hospitals.