om as , F e r na n d o G on zález Candelas, SeqCOVID-SPAIN consortium, Tanja Stadler & Richard A. NeherThis is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

This widespread occurrence of ESBL-producing Enterobacteriaceae suggests that the community could act as a reservoir and that food could contribute to the spread of these strains.

No abstract

In this study, we investigated the population structure of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in Spain and determined possible associations between specific multilocus sequence typing (MLST) types and ESBL types. Ninety-two ESBL-producing E. coli isolates from 11 Spanish hospitals were studied. The predominant ESBLs in this collection were CTX-M-14 (45.7%), SHV-12 (21.7%) and CTX-M-9 (20.6%). Phylogenetic groups and MLST types were studied. Thirty-seven isolates (40.2%) belonged to phylogroup A, 26 (28.3%) to group B1, 13 (14.1%) to group B2 and 16 (17.4%) to group D. Fifty-six sequence types (STs) were identified, but ST131 (eight isolates) and ST167 (five isolates) were the most prevalent. The most common ST complexes were ST10 (13 isolates; 14.3%) and ST23 (10 isolates; 11%). Escherichia coli ST131 carried six different ESBLs (CTX-M-1, CTX-M-9, CTX-M-10, CTX-M-14, CTX-M-15 and SHV-12), E. coli ST10 complex carried five ESBLs and E. coli ST23 complex carried four ESBLs. A great diversity of MLST types was observed among Spanish ESBL-producing E. coli isolates.

A new CTX-M-type ␤-lactamase (CTX-M-9) has been cloned from a clinical cefotaxime-resistant Escherichia coli strain. Despite the close identity that exists between the CTX-M-9 and Toho-2 ␤-lactamases (88%), the 35 amino acids located between residues Ala-185 and Ala-219 are totally different in both enzymes. Outside of this region there are only six amino acids substitutions between both proteins.Not long after the beginning of the use of the extendedspectrum ␤-lactam antibiotics, extended-spectrum ␤-lactamases (ESBLs) were detected in Europe and the United States and have now become a serious problem around the world. ESBLs are most often derivatives of TEM or SHV enzymes. However, there is a small growing family of plasmid-mediated ESBLs of Ambler class A that are not closely related to TEM or SHV ␤-lactamases but that show homology to chromosomal ␤-lactamases of Klebsiella oxytoca, including CTX-M-1 (MEN-1) (3, 5-7), CTX-M-2 (4, 6), CTX-M-3 (14), CTX-M-4 (12, 13), 20), Toho-1 (15), Toho-2 (17), and two different enzymes, both designated CTX-M-5, which will be referred to here as CTX-M-5 (8) and 20). In this report we present a new ␤-lactamase closely related to the ␤-lactamases in this family.In 1996, a cefotaxime-resistant Escherichia coli strain (785-D) against which synergy of cefotaxime with clavulanic acid was found was detected by a conventional disk diffusion susceptibility test. The strain was isolated from the urine of a 65-year-old woman who had a urinary tract infection and diabetes mellitus type 2. Two months before the isolation, the patient underwent a nephroureterectomy because of a renal carcinoma.The MICs of the ␤-lactam antibiotics were determined by the Etest (Biodisk, Solna, Sweden). The ␤-lactamase crude cell extracts were prepared from 250-ml cultures in Luria-Bertani (LB) broth (Oxoid, Basingstoke, United Kingdom). Washed, centrifuged cell pellets were subjected to three cycles of 15-s sonication treatments at 4°C, and the supernatants of the sonic extracts were frozen at Ϫ20°C until they were tested. ␤-Lactamases were characterized initially by isoelectric focusing as described previously (2) in polyacrylamide gels with a pH gradient from 4 to 11 (SERVALYT 4-9 T, 9-11 T; Serva, Heidelberg, Germany). Enzyme activities in the gel were detected by the iodometric method (2).Substrate hydrolysis in sonic extracts was monitored spectrophotometrically with a Biochrom 4060 spectrophotometer (Pharmacia, Uppsala, Sweden) as described previously (19).Conjugation studies were performed in a solid medium as described previously (19) by using E. coli 785-D (susceptible to kanamycin) and E. coli HB101 (Nal r Kan r ) as the donor and the recipient, respectively. Kanamycin (50 g/ml) and cefotaxime (4 g/ml) were used for transconjugant selection. One of the transconjugants (E. coli MSP492) was used for further experiments.Extraction of plasmid DNA was by the alkaline lysis procedure reported previously (18). Cloning of the cefotaxime resistance gene was as follows: plasmid DNA from E. coli MSP492 was pa...

hospitals (about 40,000 hospital beds) prospectively collected nonduplicate Enterobacteriaceae using the screening cutoff recommended by EUCAST. Carbapenemase characterization was performed by phenotypic methods and confirmed by PCR and sequencing. Multilocus sequencing types (MLST) were determined for Klebsiella pneumoniae and Escherichia coli. A total of 702 Enterobacteriaceae isolates met the inclusion criteria; 379 (54%) were CPE. OXA-48 (71.5%) and VIM-1 (25.3%) were the most frequent carbapenemases, and K. pneumoniae (74.4%), Enterobacter cloacae (10.3%), and E. coli (8.4%) were the species most affected. Susceptibility to colistin, amikacin, and meropenem was 95.5%, 81.3%, and 74.7%, respectively. The most prevalent sequence types (STs) were ST11 and ST405 for K. pneumoniae and ST131 for E. coli. Forty-five (54.1%) of the hospitals had at least one CPE case. For K. pneumoniae, ST11/OXA-48, ST15/OXA-48, ST405/ OXA-48, and ST11/VIM-1 were detected in two or more Spanish provinces. ST11 isolates carried four carbapenemases (VIM-1, OXA-48, KPC-2, and OXA-245), but ST405 isolates carried OXA-48 only. A wide interregional spread of CPE in Spain was observed, mainly due to a few successful clones of OXA-48-producing K. pneumoniae (e.g., ST11 and ST405). The dissemination of OXA-48-producing E. coli is a new finding of public health concern. According to the susceptibilities determined in vitro, most of the CPE (94.5%) had three or more options for antibiotic treatment. C arbapenemase-producing Enterobacteriaceae (CPE), mainly Klebsiella pneumoniae, are an emerging threat to public and individual health worldwide. These microorganisms are often resistant to almost all available antibiotics (1, 2), so there are few alternative treatment options. The most common carbapenemases are KPC (class A); VIM, IMP, and NDM (class B); and the OXA-48 types (class D). However, the extent to which health care systems have been affected and the carbapenemase types that are predominant differ substantially from country to country (3).A multicenter study performed in Spain in 2009 revealed 43 (0.04%) cases of CPE, which were mostly VIM-1 and IMP-22 (4). After that, we reported a rapid increase in the number of cases of CPE, mainly OXA-48-producing K. pneumoniae, in this country from 2010 to 2012 (5-7).Because previous studies (5, 6) were based on voluntary reports without taking into account key important issues, in this paper, we present data on the impact of CPE as obtained from a prospective, multicenter, and population-based study. We show that carbapenemase production in this country is widely and irregularly distributed; however, the rates of susceptibility to meropenem and colistin were still high.(The preliminary results of this study were presented in part at the 24th European Congress of Clinical Microbiology and Infectious Diseases Annual Meeting, 10 to 13 May 2014 in Barcelona, Spain,).

Trends in resistance to antimicrobial agents used for therapy have been evaluated with 3,797 enteropathogenic bacteria, Campylobacter, Salmonella, Shigella, and Yersinia, between 1985-1987 and 1995-1998. The greater increase in the rate of resistance was observed in Campylobacter jejuni for quinolones (from 1 to 82%) and tetracycline (from 23 to 72%) and in gastroenteric salmonellae for ampicillin (from 8 to 44%), chloramphenicol (from 1.7 to 26%), and trimethoprim-sulfamethoxazole and nalidixic acid (from less than 0.5 to 11%). Multidrug resistance was detected in several Salmonella serotypes. In the 1995-1998 period, 76% of Shigella strains were resistant to trimethoprim-sulfamethoxazole, 43% were resistant to ampicillin, and 39% were resistant to chloramphenicol. Seventy-two percent of Yersinia enterocolitica O3 strains were resistant to streptomycin, 45% were resistant to sulfonamides, 28% were resistant to trimethoprim-sulfamethoxazole, and 20% were resistant to chloramphenicol.

Group A streptococcus (GAS) has been described as an emerging cause of severe invasive infections. A retrospective hospital-based study was conducted, including GAS isolates causing invasive or non-invasive infections from January 1999 to June 2003 in Barcelona. Demographic and clinical information on the invasive cases was obtained from medical files. GAS isolates collected from 27 patients with invasive infections and 99 patients with non-invasive infections were characterized by emm type and subtype, superantigen (SAg) gene profile (speA-C, speF-J, speL, speM, ssa and smeZ), allelic variants of speA and smeZ genes, antibiotic susceptibility and genetic resistance determinants. The most prevalent emm type was emm1 (17?5 %), followed by emm3 (8?7 %), emm4 (8?7 %), emm12 (7?1 %) and emm28 (7?1 %). The smeZ allele and SAg gene profiles were closely associated with the emm type. The speA2, speA3 and speA4 alleles were found in emm1, emm3 and emm6 isolates, respectively. Overall, 27?8, 25?4 and 11?9 % of isolates were resistant to erythromycin, tetracycline or both agents, respectively. Reduced susceptibility to ciprofloxacin and levofloxacin (MIC 2-4 mg ml "1 ) was found in 3?2 % of isolates. mef(A)-positive emm types 4, 12 and 75, and erm(B)-positive emm types 11 and 25 were responsible for up to 80 % of the erythromycin-resistant isolates. No significant differences in emm-type distribution, SAg gene profile or resistance rates were found between invasive and non-invasive isolates. The SAg and antibiotic resistance genes appeared to be associated with the emm type and were independent of the disease type. INTRODUCTIONGroup A streptococcus (GAS) is a human pathogen that is responsible for a wide array of infections, varying in severity from acute pharyngitis and impetigo to severe invasive infections such as necrotizing fasciitis (NF) and streptococcal toxic shock syndrome (STSS) (Cunningham, 2000).The resurgence and persistence of severe forms of GAS diseases reported since the mid 1980s (Hoge et al., 1993;Stevens, 2002) has motivated intensive research on epidemiological, microbiological and clinical aspects of invasive GAS disease. Several factors have been considered to explain differences in disease frequency and severity, including changes in the virulence of the bacterium (Banks et al., 2002;Musser et al., 1993) and the role of host immunity (Å kesson et al., 2004;Basma et al., 1999;Kotb et al., 2002; NorrbyTeglund et al., 2000).Among the many factors involved in the virulence of the pathogen, the M protein and a group of exotoxins known as streptococcal superantigens (SAgs) have received considerable attention. Sequence analysis of the emm gene (encoding the M protein) has become an important surveillance tool for investigating the dynamics of GAS infection and more than 150 emm gene sequence types and several emm subtypes have been documented (Facklam et al., 2002;Li et al., 2003).SAgs are thought to contribute to the pathogenesis of severe GAS infections by virtue of their potent immunostimulatory activ...