[This corrects the article DOI: 10.3389/fmicb.2022.918362.].

ObjectivesCARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.MethodsIn total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC > 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.ResultsIn total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients. The main carbapenemase genes identified in CP-Kpn were blaOXA–48 (263/377), blaKPC–3 (62/377), blaVIM–1 (28/377), and blaNDM–1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).ConclusionThis study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3.

Objectives: The genus Enterobacter is a common cause of nosocomial infections. Historically, the most frequent Enterobacter species were those of Enterobacter cloacae complex and Enterobacter aerogenes. In 2019, E. aerogenes was re-classified as Klebsiella aerogenes owing to its higher genotypic similarity with the genus Klebsiella. Our objective was to characterise and compare the clinical profiles of bacteraemia caused by E. cloacae and K. aerogenes. Methods: This 3-year multicentre, prospective cohort study enrolled consecutive patients with bacteraemia by E. cloacae or K. aerogenes. Baseline characteristics, bacteraemia features (source, severity, treatment), antibiotic susceptibility, resistance mechanisms and mortality were analysed. Results: The study included 285 patients with bacteraemia [196 (68.8%) E. cloacae and 89 (31.2%) K. aerogenes]. The groups showed no differences in age, sex, previous use of invasive devices, place of acquisition, sources or severity at onset. The Charlson score was higher among patients with E. cloacae bacteraemia [2 (1-4) vs. 1 (0.5-3); P = 0.018], and previous antibiotic therapy was more common in patients with K. aerogenes bacteraemia (57.3% vs. 41.3%; P = 0.01). Mortality was 19.4% for E. cloacae and 20.2% for K. aerogenes ( P = 0.869). Antibiotic susceptibility was similar for both species, and the incidence of multidrug resistance or ESBL production was low (6% and 5.3%, respectively), with no differences between species. Conclusion: Bacteraemias caused by E. cloacae and K. aerogenes share similar patient profiles, presentation and prognosis. Patients with E. cloacae bacteraemia had more co-morbidities and those with K. aerogenes bacteraemia had received more antibiotics. (c) 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

Background: Enterobacter is among the main etiologies of hospital-acquired infections. This study aims to identify the risk factors of acquisition and attributable mortality of Enterobacter bacteremia. Methods: Observational, case-control study for risk factors and prospective cohort for outcomes of consecutive cases with Enterobacter bacteremia. This study was conducted in five hospitals in Spain over a three-year period. Matched controls were patients with negative blood cultures and same sex, age, and hospitalization area. Results: The study included 285 cases and 570 controls. E. cloacae was isolated in 198(68.8%) cases and E. aerogenes in 89(31.2%). Invasive procedures (hemodialysis, nasogastric tube, mechanical ventilation, surgical drainage tube) and previous antibiotics or corticosteroids were independently associated with Enterobacter bacteremia. Its attributable mortality was 7.8%(CI95%2.7-13.4%), being dissimilar according to a McCabe index: non-fatal-3.2%, ultimately fatal=12.9% and rapidly fatal=0.12%. Enterobacter bacteremia remained an independent risk factor for mortality among cases with severe sepsis or septic shock (OR 5.75 [CI95%2.57-12.87], p<0.001), with an attributable mortality of 40.3%(CI95%25.7-53.3). Empiric therapy or antibiotic resistances were not related to the outcome among patients with bacteremia. Conclusions: Invasive procedures, previous antibiotics and corticosteroids predispose to acquire Enterobacter bacteremia. This entity increases mortality among fragile patients and those with severe infections. Antibiotic resistances did not affect the outcome. (C) 2019 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Cumulative susceptibility reports are a valuable tool for the empirical treatment of urinary tract infections, especially in the current context of increasing resistance rates. Our objective was to analyze the antimicrobial susceptibility of bacterial isolates in urine cultures of pediatric patients during a five-year period. Retrospective study of urine cultures from 2011 to 2015. Identification and antimicrobial susceptibility tests were performed using the Vitek-2 system (BioMérieux®) and categorized according to EUCAST criteria. Antimicrobial susceptibility data were analyzed by gender and age groups (neonates, 1 month to 5 years, 5–15 years) before being compared with data obtained from patients over the age of 15 years. During the study period, 17 164 urine cultures were processed from 7924 patients under 16 years of age. Antimicrobial susceptibility rates in these patients were: ampicillin 36.3%, amoxicillin/clavulanic acid 75.3%, cefuroxime 83.2%, co-trimoxazole 68.9%, ciprofloxacin 85.3%, fosfomycin 85.5%, nitrofurantoin 84.4% and 3rd generation cephalosporins 89–91%. Aminoglycosides (>92%) and carbapenems (95%) maintained the highest susceptibility rates. The prevalence of ESBL-producing isolates was significantly lower in children under the age of 16 years (1.5% vs. 4.1%). In patients under the age of 16 years, Escherichia coli isolates in girls were significantly more sensitive (p < 0.0001) to ampicillin (41% vs. 30%) and amoxicillin/clavulanic acid (82% vs. 72%) than in boys. The compilation of cumulative susceptibility reports disaggregated by age or gender reveals significant differences. In our setting, cefuroxime may be considered the first-line empirical treatment in pediatric patients. Los informes de sensibilidad acumulada son una herramienta valiosa para guiar el tratamiento empírico de infecciones urinarias, sobre todo en el contexto actual de crecientes tasas de resistencia. Nuestro objetivo es analizar la sensibilidad antimicrobiana de bacterias aisladas de urocultivos de pacientes pediátricos durante un período de 5 años. Estudio retrospectivo de los urocultivos del período 2011-2015. La identificación y estudios de sensibilidad se realizaron con el sistema Vitek-2 (BioMérieux®) y se interpretaron según los criterios de EUCAST. Se analizaron los datos de sensibilidad antimicrobiana según sexo y tramos de edad (neonatos, 1 mes-5 años, 5-15 años) y se compararon con los datos de mayores de 15 años. En el período analizado se procesaron 17.164 urocultivos de 7.924 pacientes menores de 16 años. Los porcentajes de sensibilidad en estos pacientes fueron: ampicilina 36,3%; amoxicilina/clavulánico 75,3%; cefuroxima 83,2%; cotrimoxazol 68,9%; ciprofloxacino 85,3%; fosfomicina 85,5%; nitrofurantoína 84,4%, y cefalosporinas de tercera generación 89-91%. Aminoglucósidos (>92%) y carbapenemas (95%) mantienen las mayores tasas de sensibilidad. La prevalencia de aislamientos productores de BLEE fue significativamente menor en niños menores de 16 años (1,5% vs. 4,1%). En menores de 16 años, los aislamientos de Escherichia coli procedentes de mujeres fueron significativamente (p < 0,0001) más sensibles a ampicilina (41% vs. 30%) y amoxicilina-clavulánico (82% vs. 72%) que en varones. La elaboración de informes de sensibilidad acumulados desglosados por edad o sexo permite detectar importantes diferencias. En nuestra área, cefuroxima puede considerarse como primera opción de tratamiento empírico en pacientes pediátricos.

Corynebacterium striatum is a nosocomial opportunistic pathogen increasingly associated with a wide range of human infections and is often resistant to several antibiotics. We investigated the susceptibility of 63 C. striatum isolated at the Farhat-Hached hospital, Sousse (Tunisia), during the period 2011–2014, to a panel of 16 compounds belonging to the main clinically relevant classes of antimicrobial agents. All strains were susceptible to vancomycin, linezolid, and daptomycin. Amikacin and gentamicin also showed good activity (MICs90 = 1 and 2 mg/L, respectively). High rates of resistance to penicillin (82.5%), clindamycin (79.4%), cefotaxime (60.3%), erythromycin (47.6%), ciprofloxacin (36.5%), moxifloxacin (34.9%), and rifampicin (25.4%) were observed. Fifty-nine (93.7%) out of the 63 isolates showed resistance to at least one compound and 31 (49.2%) were multidrug-resistant. Twenty-nine resistance profiles were distinguished among the 59 resistant C. striatum. Most of the strains resistant to fluoroquinolones showed a double mutation leading to an amino acid change in positions 87 and 91 in the quinolone resistance-determining region of the gyrA gene. The 52 strains resistant to penicillin were positive for the gene bla, encoding a class A β-lactamase. Twenty-two PFGE patterns were identified among the 63 C. striatum, indicating that some clones have spread within the hospital.

Corynebacterium striatum is an opportunistic pathogen, often multidrug-resistant, which has been associated with serious infections in humans. Aminoglycosides are second-line or complementary antibiotics used for the treatment of Corynebacterium infections. We investigated the susceptibility to six aminoglycosides and the molecular mechanisms involved in aminoglycoside resistance in a collection of 64 Corynebacterium striatum isolated in our laboratory during the period 2005-2009. Antimicrobial susceptibility was determined using E-test. The mechanisms of aminoglycoside resistance were investigated by PCR and sequencing. The 64 C. striatum were assessed for the possibility of clonal spreading by Pulsed-field Gel Electrophoresis (PFGE). Netilmicin and amikacin were active against the 64 C. striatum isolates (MICs90 = 0.38 and 0.5 mg/L, respectively). Twenty-seven of the 64 C. striatum strains showed a MIC90 for kanamycin > 256 mg/L, and 26 out the 27 were positive for the aph(3')-Ic gene. Thirty-six out of our 64 C. striatum were streptomycin resistant, and 23 out of the 36 carried both the aph(3")-Ib and aph(6)-Id genes. The gene aac(3)-XI encoding a new aminoglycoside 3-N acetyl transferase from C. striatum was present in 44 out of the 64 isolates, all of them showing MICs of gentamicin and tobramycin > 1 mg/L. CS4933, a C. striatum showing very low susceptibility to kanamycin and streptomycin, contains an aminoglycoside resistance region that includes the aph(3')-Ic gene, and the tandem of genes aph(3")-Ib and aph(6)-Id. Forty-six major PFGE types were identified among the 64 C. striatum isolates, indicating that they were mainly not clonal. Our results showed that the 64 clinical C. striatum were highly resistant to aminoglycosides and mostly unrelated.

Bordetella bronchiseptica is a well-known veterinary pathogen, but its implication in human disease is probably not fully recognized. The purpose of this study was to determine the clinical significance of 36 B. bronchiseptica isolates from respiratory samples of 22 patients. Therefore, we describe microbiological characteristics, including phenotypic and genotypic identification as well as antimicrobial susceptibilities of the isolates. Clonal relatedness was evaluated using pulsed-field gel electrophoresis (PFGE). Most of the patients had some underlying immunosuppressive condition. Eighteen out of 22 (82%) patients had respiratory symptoms, and the death of 2 patients was associated with respiratory infection.All strains were correctly identified at species level by the simultaneous use of phenotypic methods and were confirmed by specific amplification of the upstream region of the fla gene. Tigecycline, minocycline, doxycycline, colistin, and meropenem were the most active agents tested. PFGE analysis revealed that repeated infections involving each patient had been caused by the same strain.

Recurrent bloodstream infections caused by a Gram-positive bacterium affected an immunocompromised child. Tsukamurella pulmonis was the microorganism identified by secA1 gene sequencing. Antibiotic treatment in combination with removal of the subcutaneous port healed the patient.

Acinetobacter baumannii is one of the most important antibiotic-resistant nosocomial bacteria. We investigated changes in the clinical and molecular epidemiology of A. baumannii over a 10-year period. We compared the data from 2 prospective multicenter cohort studies in Spain, one performed in 2000 (183 patients) and one in 2010 (246 patients), which included consecutive patients infected or colonized by A. baumannii. Molecular typing was performed by repetitive extragenic palindromic polymerase chain reaction (REP-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST).The incidence density of A. baumannii colonization or infection increased significantly from 0.14 in 2000 to 0.52 in 2010 in medical services (p<0.001). The number of non-nosocomial health care-associated cases increased from 1.2% to 14.2%, respectively (p<0.001). Previous exposure to carbapenems increased in 2010 (16.9% in 2000 vs 27.3% in 2010, p=0.03). The drugs most frequently used for definitive treatment of patients with infections were carbapenems in 2000 (45%) and colistin in 2010 (50.3%). There was molecular-typing evidence of an increase in the frequency of A. baumannii acquisition in non-intensive care unit wards in 2010 (7.6% in 2000 vs 19.2% in 2010, p=0.01). By MSLT, the ST2 clonal group predominated and increased in 2010. This epidemic clonal group was more frequently resistant to imipenem and was associated with an increased risk of sepsis, although not with severe sepsis or mortality.Some significant changes were noted in the epidemiology of A. baumannii, which is increasingly affecting patients admitted to conventional wards and is also the cause of non-nosocomial health care-associated infections. Epidemic clones seem to combine antimicrobial resistance and the ability to spread, while maintaining their clinical virulence.

ABSTRACT A carbapenem-resistant Acinetobacter pittii strain carrying an OXA-24-like enzyme was isolated in northern Spain in 2008. Sequence analysis confirmed the presence of the novel bla OXA-207 gene flanked by the site-specific XerC/XerD-like recombination binding sites and showing a unique Gly222Val substitution compared to OXA-24. Cloning and kinetic analysis showed that OXA-207 presents a reduction in the catalytic efficiency against carbapenems and a noticeable increase for oxacillin.

Most Escherichia coli resistant to quinolones are not haemolytic. The objective of this study was to determine the phylogroup, clonal relationship, mechanism of quinolone resistance and virulence factors in 70 haemolytic E. coli resistant to nalidixic acid. Sixty-six isolates contained the hlyA gene, belonged to phylogroup B2, and 61 of them presented low-level resistance to fluoroquinolones. Four isolates presented high-level resistance to fluoroquinolones, contained the clyA gene and were included in phylogroup D. One single isolate (phylogroup D, with low level resistance to fluoroquinolones) contained both cytotoxins.

The aim of this study was to assess the phenotypic and genotypic diversity of 56 Arcanobacterium haemolyticum isolates isolated from 51 patients attending primary health care centres and emergency units in the health area of Santander (Cantabria, northern Spain). Phenotypic characterization was based on morphological, biochemical, and antigenic tests. Species identification was confirmed by amplification and sequencing of the 16S rDNA gene. Antimicrobial susceptibility testing was determined by microdilution following the Clinical and Laboratory Standards Institute recommendations for coryneform bacteria. Genetic diversity was evaluated using BOX-PCR and pulsed-field gel electrophoresis. Eighty percent of the isolates had an identical BOX-PCR pattern, suggesting the spread of a single clone. The present report provides extensive information on the phenotypic and genotypic characterization of A. haemolyticum.

ABSTRACT The accuracy of the MicroScan WalkAway, BD Phoenix, and Vitek-2 systems for susceptibility testing of quinolones and aminoglycosides against 68 enterobacteria containing qnrB , qnrS , and/or aac(6 ′)-Ib-cr was evaluated using reference microdilution. Overall, one very major error (0.09%), 6 major errors (0.52%), and 45 minor errors (3.89%) were noted.

In 1998, the first plasmid-mediated gene involved in quinolone resistance (currently named qnrA1 ) was reported. Extra qnr -like plasmid-mediated genes ( qnrB , qnrS , qnrC , qnrD ) and their chromosomal homologues have also been characterized. These genes code for a pentapeptide repeat protein that protects type II topoisomerases from quinolones. Since then, there have been reports of two other plasmid-mediated resistance mechanisms: the modification of quinolones with a piperazinyl substituent by the acetyltransferase, Aac(6′)-Ib-cr; and active efflux by QepA and OqxAB, pumps related to major facilitator superfamily (MFS) transporters. These genes have a wide geographic distribution (mainly in Enterobacteriaceae ). Because of the difficulties of phenotypic detection of this type of resistance, its real prevalence is only partially known. One important point is that although these mechanisms cause only low-level resistance, they favor and complement the selection of other resistance mechanisms.

Implementation of surveillance culture programs and molecular typing are important contributions of Clinical Microbiology to the control of nosocomial infections. This document provides information on collection, transport, preservation, and processing of samples for surveillance culture, as well as the criteria for interpreting and reporting the results of relevant etiologic agents in nosocomial infection. This includes methicillin-resistant Staphylococcus aureus (MRSA), glycopeptide-resistant Enterococcus spp., enterobacteria producing extended-spectrum beta -lactamases (ESBLs), multiresistant Acinetobacter baumannii and carbapenem-resistant Pseudomonas aeruginosa. Details on the available methods for rapid diagnosis are also presented. The information in this document attempts to provide a general approach to the problem and may be considered a starting point for laboratories that are developing their own guidelines, according to needs defined by the multidisciplinary nosocomial infection control team.

BACKGROUND:Most cases of invasive group A streptococcal (GAS) disease arise sporadically in the community, but outbreaks of severe invasive GAS infections have been reported in closed environments, such as military populations, family communities and hospitals. An outbreak of invasive GAS disease involving 3 cases of streptococcal toxic shock syndrome (TSS), one with a fatal course, occurred among children attending a day-care center located in Cantabria, Northern Spain.OBJECTIVE:To determine the characteristics of GAS isolates obtained from the outbreak environment.METHODS:GAS isolates obtained from children attending the same day-care facility, staff members, and family contacts were assayed for emm typing, pulse-field gel electrophoresis (PFGE), and toxin-gene content. One isolate obtained from the fatal case was also characterized by multilocus sequence typing. Antimicrobial susceptibility testing was done. Strains from patients unrelated to the outbreak were included for comparison.RESULTS:All GAS isolates from children attending the day-care center, including those from streptococcal TSS cases, shared the same emm type 4, genomic pattern by PFGE (A) and toxin-gene profile. Neither the emm type nor the PFGE pattern or toxin gene profile of the outbreak-associated strains were encountered among GAS isolated from household or staff contacts.CONCLUSIONS:A clone of GAS belonging to emm type 4 and characterized by a specific PFGE pattern and toxin-gene profile was responsible for a community outbreak of streptococcal TSS disease in a child day-care center in Spain. This is the first day-care outbreak reported in our country.