Blood Culture Isolates Research Articles

In Vitro Activity of Ceftolozane-Tazobactam against Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa Obtained from Blood Cultures from Sentinel Public Hospitals in South Africa.

Multidrug-resistant (MDR) Gram-negative bacteria are responsible for the majority of healthcare-associated infections and pose a serious threat as they complicate and prolong clinical care. A novel cephalosporin-β-lactamase-inhibitor combination, ceftolozane-tazobactam (C/T) was introduced in 2014, which improved the treatment of MDR pathogens. This study aimed to evaluate the activity of C/T against Escherichia coli (n = 100), Klebsiella pneumoniae (n = 100), and Pseudomonas aeruginosa (n = 100) blood culture isolates in South Africa (SA). Isolates were sequentially selected (2010 to 2020) from the Group for Enteric, Respiratory, and Meningeal Diseases Surveillance (GERMS) programme in SA. Organism identification was performed using the matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) instrument (Microflex, Bruker Daltonics, Bremen, Germany), and antibiotic susceptibility was performed using the Sensititre instrument (Trek Diagnostic Systems, East Grinstead, UK). C/T resistance was reported in 16 E. coli, 28 K. pneumoniae and 13 P. aeruginosa isolates. Fifty percent of the C/T resistant isolates were subjected to whole-genome sequencing (WGS). According to the whole genome multilocus sequence typing (MLST) analysis, the E. coli isolates (n = 8) belonged to sequence type (ST)10, ST131, ST405, and ST410, the K. pneumoniae isolates (n = 14) belonged to ST1, ST37, ST73, ST101, ST231, ST307, ST336 and ST6065 (novel ST), and the P. aeruginosa isolates (n = 7) belonged to ST111, ST233, ST273, and ST815. The WGS data also showed that all the E. coli isolates harboured aminoglycoside (aph (3'')-Ib, aph (6)-Id), macrolide (mdfA, mphA), and sulphonamide (sul2) antibiotic resistance genes, all the K. pneumoniae isolates harboured β-lactam (blaCTX-M-15), and sulphonamide (sul2) antibiotic resistance genes, and all the P. aeruginosa isolates harboured aminoglycoside (aph (3')-IIb), β-lactam (PAO), fosfomycin (fosA), phenicol (catB7), quinolone (crpP), and disinfectant (qacE) antibiotic resistance genes. It is evident that E. coli, K. pneumoniae and P. aeruginosa can adapt pre-existing resistance mechanisms to resist newer β-lactam molecules and inhibitors, since these isolates were not exposed to ceftolozane-tazobactam previously.

Evaluation of a MALDI-TOF MS cephalosporinase assay for blood culture isolates

Objectives: Rapid detection of beta-lactamases has the potential to improve antimicrobial stewardship and sepsis outcomes. The aim of this study was to evaluate a recently TGA-approved cephalosporinase detection method utilising matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) on blood culture isolates. This was compared to standard antimicrobial susceptibility testing and phenotypic cephalosporinase detection. Methods: A total of 114 gram negative blood culture isolates were retrospectively analysed. Isolates were selected to either be ceftriaxone non-susceptible by Vitek 2 semi-automated system (version 08.01; bioMerieux, USA, AST-N246 card) (n=31) and/or demonstrate an inducible cephalosporinase or ESBL on disc approximation testing (n=32). This cohort was compared to an equal number of ceftriaxone-susceptible isolates by Vitek 2 (n=57). The range of organisms included Escherichia coli (n=62), followed by Serratia marcescens (n=12), Pseudomonas aeruginosa (n=11), Enterobacter cloacae complex (n=10), Klebsiella aerogenes (n=5), Klebsiella pneumoniae (n=3), Klebsiella oxytoca (n=3), Morganella morganii (n=3), Acinetobacter calcoaceticus-A. baumannii complex (n=3), and Citrobacter freundii (n=2). Sub-cultured colonies were prepared with the MBT STAR-Cepha IVD Kit and third-generation cephalosporin hydrolysis was detected using the MBT STAR-BL IVD Module (Bruker Daltronics) on MALDI-TOF MS after 30 min incubation time. Results: The MALDI-TOF MS assay sensitivity and specificity for third-generation cephalosporinase activity was 61.3% and 77.1% respectively. The assay detected 11/11 (100%) ESBL producers and 5/6 (83.3%) AmpC type third-generation cephalosporinase producers. Additionally, third generation cephalosporinase activity was detected by the MALDI-TOF MS assay in 17 of 26 inducible cephalosporinase positive isolates (65.4%) that tested susceptible to ceftriaxone by Vitek 2. Of all species included, Pseudomonas aeruginosa had the lowest concordance of MALDI-TOF MS and Vitek 2 results, with only 1/11 isolates (9%) positive by MALDI-TOF MS. Conclusions: Overall the MALDI-TOF MS cephalosporinase assay lacked sensitivity in detection of third generation cephalosporinases compared to antimicrobial susceptibility testing by Vitek 2. The risk for false negative results in screening for resistance in blood culture isolates is too high to consider its implementation in the standard workflow, although there may be possible benefit in detecting ESBL and ampC type cephalosporinase activity following species identification as an alternative to standard disc approximation testing.

Genotypic resistance determined by whole genome sequencing versus phenotypic resistance in 234 Escherichia coli isolates

Whole genome sequencing (WGS) enables detailed characterization of bacteria at single nucleotide resolution. It provides data about acquired resistance genes and mutations leading to resistance. Although WGS is becoming an essential tool to predict resistance patterns accurately, comparing genotype to phenotype with WGS is still in its infancy. Additional data and validation are needed. In this retrospective study, we analysed 234 E. coli isolates from positive blood cultures using WGS as well as microdilution for 11 clinically relevant antibiotics, to compare the two techniques. We performed whole genome sequencing analyses on 234 blood culture isolates (genotype) to detect acquired antibiotic resistance. Minimal inhibitory concentrations (MIC) for E. coli were performed for amoxicillin, cefepime, cefotaxime, ceftazidime, meropenem, amoxicillin/clavulanic acid, piperacillin/tazobactam, amikacin, gentamicin, tobramycin, and ciprofloxacin, using the ISO 20776-1 standard broth microdilution method as recommended by EUCAST (phenotype). We then compared the two methods for statistical ‘agreement’. A perfect (100%) categorical agreement between genotype and phenotype was observed for gentamicin and meropenem. However, no resistance to meropenem was observed. A high categorical agreement (> 95%) was observed for amoxicillin, cefepime, cefotaxime, ceftazidime, amikacin, and tobramycin. A categorical agreement lower than 95% was observed for amoxicillin/clavulanic acid, piperacillin/tazobactam, and ciprofloxacin. Most discrepancies occurred in isolates with MICs within ± 1 doubling dilution of the breakpoint and 22.73% of the major errors were samples that tested phenotypically susceptible at higher antibiotic exposure and were therefore considered as ‘not resistant’. This study shows that WGS can be used as a valuable tool to predict phenotypic resistance against most of the clinically relevant antibiotics used for the treatment of E. coli bloodstream infections.

Epidemiology and mortality outcome of carbapenem- and colistin-resistant Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa bloodstream infections

BackgroundBloodstream infections caused by carbapenem-resistant Gram-negative bacteria represent a major therapeutic challenge to clinicians worldwide. This study examined the epidemiology of carbapenem and colistin resistance in Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii blood isolates in an academic institution in Oman. MethodsAdult patients with bloodstream infections caused by Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii, between January 1, 2017, and December 31, 2020, were identified. Rates of carbapenem resistance, carbapenem-colistin dual resistance, and 30-day all-cause mortality were examined. Results585 non-repeat bloodstream infections due to Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii were identified during the study period. OXA-48 was the most prevalent carbapenemase gene in carbapenem-resistant K. pneumoniae blood isolates. Carbapenem resistance was observed in 160 (27.7%) of blood isolates, with 131 (81.9%) of these being healthcare-onset cases. Carbapenem resistance was highest in Acinetobacter baumannii (80.4%), followed by Klebsiella pneumoniae (46.4%), and Pseudomonas aeruginosa (29.9%). Sixteen (13.4%) of the carbapenem-resistant blood isolates were found to be colistin resistant. Thirty-day all-cause mortality was 68.1% in patients with bloodstream infections caused by carbapenem-resistant isolates, versus 21.3% in patients with bloodstream infections caused by carbapenem-susceptible isolates. ConclusionThe prevalence of carbapenem resistance and carbapenem-colistin dual resistance in Gram-negative blood culture isolates from patients with bloodstream infections is unacceptably high. Patients with bloodstream infections due to carbapenem-resistant isolates had substantially higher mortality.

No Significant Differences in Presepsin Levels According to the Causative Microorganism of Bloodstream Infection.

CD14 recognizes lipopolysaccharide (LPS), and presepsin is a fragment of soluble CD14. Still, it remains uncertain whether Gram-negative bacteria induce higher presepsin levels than other microorganisms. To address this question, this study aimed to analyze presepsin levels based on microorganisms isolated in blood cultures. This study was a single-center study comprising suspected sepsis patients enrolled from July 2020 to September 2020. A total of 95 patients with a single isolate confirmed in blood culture were analyzed to evaluate if there are any differences in presepsin levels according to microbial isolates. Plasma presepsin level was measured using PATHFAST assay kit and analyzer (LSI Medience Corporation, Tokyo, Japan). There were 26 Gram-positive bacteremia, 65 Gram-negative bacteremia, and 3 fungemia patients with median presepsin levels of 869, 1,439, and 11,951 pg/mL, respectively. Besides, one case of algaemia demonstrated a presepsin level of 1,231 pg/mL. Our results showed no statistically significant difference in presepsin levels among patients with Gram-positive bacteremia, Gram-negative bacteremia, and fungemia. Furthermore, presepsin levels did not differ significantly among bloodstream infections caused by bacteria that were isolated from at least three different patients. In particular, Gram-positive bacteria such as Staphylococcus aureus and Enterococcus faecalis were able to induce presepsin levels comparable to those induced by Gram-negative bacteria. We demonstrated that there were no significant differences in plasma presepsin levels according to microbial isolates in blood culture. The major cause of the variability in presepsin levels during bloodstream infection might be the immunogenicity of each microorganism rather than the presence of LPS in the microorganism.

In Vitro Detection of Virulence Factors of Candida albicans & non-albicans Candida species Isolated from the Samples in ICU Patients

Aim: To isolate and identify Candida albicans and non-albicans Candida from various clinical specimen of Intensive care Unit and to investigate some virulence factors and perform their Anti- fungal susceptibility. Materials and Methods: Overall 32 isolates (12 Candida albicans and 20 non- albicans Candida spp.) were included in this study. Virulence factors were studied. In isolates, egg yolk agar was used for determining phospholipase activity, while sheep and human plasma used to determine coagulase activity, Sabouraud dextrose agar with sheep blood for hemolysin activity. Biofilm formation was detected by the tube adherence method. Results: In both Candida spp., it was found that hemolytic activity were higher next to phospholipases activity. It was also found that Coagulase activity were detected in Candida species found to be higher with sheep plasma compared to human plasma. Biofilm production was found to be less and mostly were from blood culture isolates. Conclusion: Knowledge of these virulence factors is an important tool to understand pathogenesis of candidiasis and in addition will help to explore new antifungal drug targets for improved therapeutic regimens.

Bacteriological profile of blood culture isolation and their antibiotic susceptibility pattern in BIMR Hospital, Gwalior, India

Bacteriological profile of blood culture isolation and their antibiotic susceptibility pattern in BIMR Hospital, Gwalior, India

Bacteriological profile of blood culture isolation and their antibiotic susceptibility pattern in BIMR Hospital, Gwalior, India

Bacteriological profile of blood culture isolation and their antibiotic susceptibility pattern in BIMR Hospital, Gwalior, India

Bacteriological profiles and antibiotic susceptibility of neonatal sepsis in a university hospital of Northern India.

Knowledge of epidemiology of bacterial isolates and their anti-biograms in hospital settings is necessary for prompt empirical anti-microbial therapy of neonatal sepsis. To study risk factors, bacteriological profiles, and anti-biograms of blood culture isolates of both early and late onset neonatal sepsis. It is a prospective observational study conducted from January 2020 till July 2021 at our tertiary care center. Neonates (0-28 days) admitted to this neonatal intensive care unit clinically suspected with sepsis were subjected to blood cultures, and the isolates were identified both biochemically and by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system. Antibiotic susceptibility testing (AST) was performed as per CLSI guidelines. Chi-square test was used. Out of 280 suspected cases of neonatal sepsis, 43 (15.3%) cases showed positive blood culture. Of these, the majority (30, 69.8%) had late-onset neonatal sepsis. Major pre-disposing risk factors were pre-term birth and a low birth weight (26, 60.5%). Gram-negative bacteria and Gram-positive bacteria were isolated in 25 (58.1%) and 18 (41.9%) blood cultures, respectively. Klebsiella pneumoniae (37.5%) was the most predominant pathogen in both early-onset (23.1%) and late-onset (46.7%) sepsis. Coagulase negative Staphylococcus (34.8%) was the second most common organism and was more common in late onset (23.2%) neonatal sepsis. A high level of antibiotic resistance was noted in Klebsiella pneumoniae isolates, even to amikacin (76.5%) and carbapenems (66.7%). Increased resistance in bacterial isolates of neonatal sepsis emphasizes the need of AST of bacterial isolates for proper antibiotic administration.

A STUDY ON CHANGING TRENDS IN ISOLATION RATE AND ANTIMICROBIAL SUSCEPTIBILITY PATTERN OF KLEBSIELLA PNEUMONIAE ISOLATES IN PEDIATRIC AND ADULT BLOOD STREAM INFECTIONS.

Back ground: Blood stream infection is defined as positive blood cultures in a patient with systemic signs of infection. Aim and objective: To identify the changing trends in isolation rate and antimicrobial susceptibility pattern of Klebsiella pneumoniae isolates from blood stream infection both in adult and paediatric patients. Materials and Methods: The study was conducted at Osmania Medical College, Hyderabad. A review analysis of 11,805 cases of clinically suspected blood stream infection was done over a period of 3 years from 2019 to 2022. The study included blood culture data from Niloufer hospital for women and children and Osmania general hospital, Hyderabad. Results: Out of 6752 paediatric blood samples 678 were culture positive contributing for 10.5% of positivity rate. Among 5053 adult blood samples 559 were culture positive contributing for 11% positivity rate. Among the blood culture isolates Klebsiella pneumoniae isolation rate was 29.79% in paediatric samples and 16.81% in adult samples. Resistance to amoxiclav is increased in Klebsiella pneumoniae isolates among paediatric age group in last three years (21%(2019), 77%(2020), 83% (2021). Significant reduction in susceptibility towards cefaperazone in Klebsiella pneumoniae isolates in adult samples which shows 100% in 2019, 47% in 2020 and 32% in 2021. Susceptibility of piperacillin/tazobactum was increased in Klebsiella pneumoniae isolates among both adult and paediatric isolates. Klebsiella pneumoniae isolates among paediatric samples sensitivity towards ciprofloxacin and gentamicin is increased, this can be explained by reduced usage of these antibiotics in paediatric population. Conclusion: Judiciary use of antimicrobial agent in clinical setting is important to reduce the emergence of drug resistant Klebsiella pneumoniae.

Phenotypic and Genomic Insights into Biofilm Formation in Antibiotic-Resistant Clinical Coagulase-Negative Staphylococcus Species from South Africa.

The work aims to investigate biofilm formation and biofilm/adhesion-encoding genes in coagulase-negative staphylococci (CoNS) species recovered from blood culture isolates. Eighty-nine clinical CoNS were confirmed using the VITEK 2 system, and antibiotic susceptibility testing of isolates was conducted using the Kirby-Bauer disk diffusion method against a panel of 20 antibiotics. Isolates were qualitatively screened using the Congo red agar medium. Quantitative assays were performed on microtiter plates, where the absorbances of the solubilised biofilms were recorded as optical densities and quantified. In all, 12.4% of the isolates were strong biofilm formers, 68.5% had moderate biofilm capacity, and 17.9% showed weak capacity. A subset of 18 isolates, mainly methicillin-resistant S. epidermidis, were investigated for adherence-related genes using whole-genome sequencing and bioinformatics analysis. The highest antibiotic resistance rates for strongly adherent isolates were observed against penicillin (100%) and cefoxitin (81.8%), but the isolates showed no resistance to linezolid (0.0%) and tigecycline (0.0%). The icaABC genes involved in biofilm formation were detected in 50% of the screened isolates. Other adherence-related genes, including autolysin gene atl (88.8%), elastin binding protein gene ebp (94.4%), cell wall-associated fibronectin-binding protein gene ebh (66.7%), clumping factor A gene clfA (5.5%), and pili gene ebpC (22.2%) were also found. The insertion sequence IS256, involved in biofilm formation, was found in 10/18 (55.5%) screened isolates. We demonstrate a high prevalence of biofilm-forming coagulase-negative staphylococci associated with various resistance phenotypes and a substantial agreement between the possession of biofilm-associated genes and the biofilm phenotype.

A Retrospective Analysis of Culture-Confirmed Enterococci Bloodstream Infections in South Africa, 2016-2020: A Cross-Sectional Study.

(1) Background: The emergence of multidrug resistance enterococci is a major public health concern. This study aimed to determine the prevalence and antimicrobial resistance of enterococci isolated from blood cultures over a five-year period (2016−2020) at public hospitals in South Africa. (2): Methods: A retrospective analysis of clinical enterococci isolated from bloodstream infection samples at the South African public hospitals was conducted. The ESKAPE dataset from January 2016 to December 2020 was obtained from the central data warehouse (CDW) at the National Health Laboratory Service (NHLS). (3): Results: Following de-duplication, a total of 130,352/306,592 organisms isolated from blood cultures were identified as ESKAPE pathogens. In this study, K. pneumoniae (25%; 33,082/130,352), was the most frequently isolated pathogen from blood cultures, followed by S. aureus (23%; 29,922/130,352) and enterococci (16%; 21,339/130,352). Of the enterococci cases, about 43% (9132/21,339) of cases were from the infants aged (<1-year old) and 32% (6745/21,339) from the adult patients. No changes observed in vancomycin, teicoplanin, and linezolid susceptibility; however, E. faecium and E. faecalis blood culture isolates remained highly susceptible (>97%) to these antibiotics. (4): Conclusions: The current study revealed a significant increase of E. faecalis and E. faecium blood culture isolates as compared to the previous national ESKAPE data. Low vancomycin resistance was observed. Continuous monitoring of antimicrobial resistant Enterococcus species is warranted in South Africa.

Comparative Evaluation of Three Phenotypic Tests-Carba NP, Modified Carba NP and Rapidec Carba NP Test for Rapid Detection of Carbapenem Resistance in Blood Culture Isolates of Escherichia coli in an ICU Setting.

To determine the antibiotic resistance pattern, the prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance in blood culture isolates of E. coli. Further, we evaluated and compared Carba NP, Modified Carba NP and a kit-based Rapidec Carba NP test to detect carbapenem resistance rapidly. Twenty-six carbapenem-resistant strains and four susceptible strains were selected. The three methods mentioned above were evaluated as per Clinical Laboratory Standards Institute (CLSI). These tests are based on biochemical detection of the hydrolysis of the beta-lactam ring of a carbapenem-imipenem, followed by the colour change of a pH indicator. Carba NP test was positive in 24 out of 26 isolates; the Modified Carba NP and Rapidec Carba NP tests were positive for all the isolates (26/26). All the carbapenemase non-producers (100%, 04/04) were negative. Modified Carba NP is a more effortless and inexpensive alternative to the Carba NP test, allowing the detection of carbapenemase activity directly from bacterial cultures of Enterobacteriaceae. The test could be used in low-income countries with large reservoirs for carbapenemase producers and can be implemented in any laboratory worldwide.

Bloodstream infection in cancer patients; susceptibility profiles of the isolated pathogens, at Khartoum Oncology Hospital, Sudan.

Bloodstream infection is one of the major causes of mortality in patients with malignancies. This study aimed to determine the local profile of blood culture isolates and their antibiotic sensitivities in febrile neutropenic cancer patients and to decide if any modifications to antibiotics policies are necessary. This is a cross-sectional study conducted between the first of October to the end of December 2018 at Khartoum Oncology Hospital, Sudan. Blood samples from febrile neutropenic patients were collected for culture. Isolates were identified, and their antimicrobial susceptibility was determined by standard laboratory procedures. Bloodstream infections were confirmed in 12 % (n = 69/569) of total blood cultures. Gram negative bacilli were the dominant causative agents (63.8%) while (36.2%) of infections were caused by gram positive cocci. Escherichia coli was the most common isolate (30.4%).The proportions of resistance among gram negative bacilli were high for cefuroxime, amoxicillin/clavulanic acid, Ceftazidime, and ceftriaxone. Extended-spectrum β-lactamase producing isolates were identified in 34.1% of the positive cultures. Gram positive cocci showed high resistance to tetracycline, penicillin and erythromycin but were completely sensitive to vancomycin and gentamicin. Most of Staphylococcus aureus isolates were methicillin resistant. Gram negative bacilli were the predominant etiologic agents of bloodstream infections in our patients. Both Gram-positive and Gram-negative bacteria showed high levels of resistance for most of the common antibiotics used for empiric treatment. Regular surveillance to study bacterial resistance patterns must be conducted to modify antibiotics stewardship in our institution.

1164. Antibacterial Utilization for Febrile Illnesses and Laboratory-Confirmed Bloodstream Infections in Northern Tanzania

Abstract Background Antimicrobial resistance is an important cause of morbidity and mortality globally; low- and middle-income countries (LMICs) face an especially high burden. Ineffective antimicrobial prescriptions and use of broad-spectrum agents contribute to resistance. We describe antibacterial prescribing patterns in patients with febrile illnesses and bloodstream infections (BSI) in northern Tanzania. Methods We compared data from two hospital-based prospective cohort studies, cohort 1 (2011-2014) and cohort 2 (2016-2019), both enrolled febrile pediatric and adult inpatients in Moshi, Tanzania. Aerobic blood culture was obtained in all patients and standard methods were used to determine isolate antimicrobial susceptibility. To describe management of febrile illness, we analyzed antibacterial drug prescription prior to and after enrollment. Broad-spectrum antibacterials were categorized using published frameworks. Treatments were categorized as discordant if a blood culture isolate was not susceptible to the patient’s antibacterial regimen. We performed descriptive statistics and logistic regression to understand predictors of receiving an antibacterial. Results In total, 2,176 febrile inpatients were enrolled. Antibacterials were administered to 430 (42.0%) and 501 (45.1%) patients prior to enrollment, and 930 (89.1%) and 1,060 (93.6%) during admission in cohorts 1 and 2, respectively. Infancy and duration of fever were associated with higher antibacterial prescribing prior to enrollment (Table 2). Broad-spectrum antibacterials were administered to 548 (52.5%) in cohort 1 and 682 (60.2%) in cohort 2. Laboratory-confirmed bacteremia was detected in 87 (4%) patients. Susceptibility results were available in 73 patients; of these, 41 (56.2%) received discordant antibacterials. Conclusion Antibacterials were commonly administered for febrile illness in outpatient and inpatient settings; over half of patients received broad-spectrum antibacterials. A high proportion of patients with culture-positive BSI were treated with ineffective antimicrobials. Improved laboratory diagnostics for febrile illness, antimicrobial stewardship interventions, context-specific clinical guidelines, and provider education may improve prescribing practices. Disclosures Julian Hertz, MD, Roche Diagnostics: Grant/Research Support.

151. Molecular diversity and resistance mechanisms of Klebsiella pneumoniae bloodstream infections in Peru

Abstract Background Klebsiella pneumoniae, a leading pathogen for mortality associated with antimicrobial resistance (AMR), was responsible for &amp;gt; 250,000 deaths in 2019. Genomic surveillance can guide the development of vaccines and new antibiotics against this pathogen. While AMR disproportionally affects low-and middle-income countries, limited genomic data are available from these countries. To close this gap, this study provides genomic characterization of K. pneumoniae blood isolates recovered in Peru. Methods Consecutive non-duplicate K. pneumoniae blood culture isolates were collected during an AMR surveillance study (VIRAPERU) from Jul 2017 to Oct 2019, from 15 tertiary hospitals from 13 regions of Peru. DNA extraction (GeneJET, Thermo Fisher Scientific), DNA library (Nextera XT, Illumina) and genome sequencing (MiSeq 500bp-V2, Illumina) were conducted. De novo assembling (SPAdes v3.13.1), quality assessment and annotation (Nullarbor v2.0), and identification of species, ST group, K/O loci, AMR (Kleborate v2.0.1) were conducted. Phylogenetic trees were built with Microreact v.192. Results From 119 K. pneumoniae isolates, 114 were recovered and confirmed to belong to the Klebsiella taxon. Six species were identified, the most prevalent being K. pneumoniae (106), followed by K. quasipneumoniae (3). Among carbapenem-resistant isolates (n=13), 10 (77%) carried the blaNDM-1 gene, while other three carried blaKPC-2 (1), blaIMP-16 (1) or no carbapenemase (1). Phenotypic co-resistance to colistin was present in 2 isolates, both negative for mcr-1 gene. The most common mechanisms of resistance to 3rd generation cephalosporins, quinolones and to aminoglycosides were CTX-M-15 (74.4%), qnrB (63.6%), aac(6')-Ib-cr (87.5%), respectively. Many other AMR genetic determinants were identified (Fig. 1). Sixty ST groups were identified, but only 6 ST groups carried a carbapenemase gene (Fig. 2). A wide diversity of K and O locus was also identified (54 distinct K-loci and 14 distinct O-loci). Figure 1.Genetic determinants of antimicrobial resistance and virulence found in Klebsiella pneumoniae blood isolates of PeruFigure 2.Distribution of ST groups according to specific antimicrobial resistance profiles Conclusion Bloodstream infections in Peru are caused by a wide diversity of K. pneumoniae strains, carrying multiple AMR genes. Carbapenem resistance is principally a result of blaNDM-1 carriage, found across 6 specific ST groups. Disclosures Omai Garner, PhD, Beckman Coulter, Inc.: Clinical trial data collection funded by Beckman Coulter, Inc. Victor Nizet, MD, Cellics Therapeutics: Advisor/Consultant|Clarametyx Biosciences: Advisor/Consultant|Vaxcyte, Inc.: Advisor/Consultant|Vaxcyte, Inc.: Grant/Research Support.

Bacterial Contamination of Neonatal Intensive Care Unit

Background and objectives. The environmental impact assessment plays an important role in ensuring environmental media. This study aimed to assess the environmental pollution of the neonatal intensive care unit in Al-Jala hospital of obstetrics and gynecology, Tripoli, Libya through environmental monitoring of bacteria on different surfaces. Methods. A cross-sectional, descriptive study was carried out in the neonatal intensive care unit from December- to February 2022 at Al-Jala hospital, Tripoli. A total of 61 samples were collected with a sterile swab from high-contact environmental surfaces. Isolation, identification, and antibiotic resistance of bacterial isolated were performed by standard technique. Blood culture isolates from neonatal intensive care unit patients were compared with the environmental isolates during the study period. Results. Out of 61 samples, bacterial growth was observed in 58 samples, out of which 40 (68.9%) were gram-positive and 18 (31.03%) were gram-negative. The observed gram-positive bacterial isolate was Staphylococcus aureus 13(32.5%), and most of gram-positive isolates were recovered from an incubator, suction tip, stethoscope, ambu bag, and staff hand. The potential gram-negative bacterial isolates were E. coli 10 (55.5%), and the majority of gram-negative isolates were recovered from the door handle, suction tip, neonate breathing tube, and staff hand. The isolated bacteria were resistant to amoxicillin (41.3%), clindamycin (39.6%), imipenem, and tetracycline (27.5%). Common potential pathogens isolated from the blood culture of NICU patients were staphylococcus aureus. Conclusion. Bacterial contamination of objects and instruments in neonatal intensive care units was high (95%). This study emphasizes the need for rigorous decontamination protocols and hand hygiene. Clindamycin and tetracycline may be used for empirical therapy in clinically suspected cases of isolates.

A Rapid Carbapenemase Genes Detection Method with Xpert Carba-R from Positive Blood Cultures Compared with NG-Test Carba 5 and Sequencing.

The objective of the current study was to evaluate the performance of Xpert Carba-R for the direct detection and identification of carbapenemase genes from positive blood cultures. Pathogens which extracted from positive blood cultures and identified using MALDI-TOF MS as Enterobacterales were included in this study. Xpert Carba-R was used for the rapid detection of carbapenemase genes from positive blood cultures. NG-Test CARBA 5 and polymerase-chain reaction (PCR) sequencing were used for the detection of carbapenemases and carbapenemase genes in positive blood culture isolates, respectively. Finally, antibiotic susceptibility tests were conducted using the VITEK-2 Compact system. A total of 133 positive blood cultures of Enterobacterales were collected and 27 of them were detected to carry carbapenemase genes using Xpert Carba-R. In comparison with PCR sequencing results, the sensitivity and specificity of Xpert Carba-R and NG-Test CARBA 5 were calculated as 100%. Additionally, Xpert Carba-R could significantly shorten the turnaround time by directly detecting positive blood cultures comparing with NG-Test CARBA 5. For 27 carbapenem-producing strains, the resistance rates of carbapenems and aztreonam were 96.3% and 92.6%, respectively. Strains carrying the blaKPC gene were all sensitive to ceftazidime-avibactam. All strains were sensitive to tigecycline and colistin. Xpert Carba-R is suitable for the rapid detection of main carbapenemase genes from positive blood cultures with high sensitivity and specificity. In comparison with NG-Test CARBA 5 and PCR sequencing methods, the timely and convenient method can be a useful test to guide optimal therapy and infection control.

Effect of resistance to third-generation cephalosporins on morbidity and mortality from bloodstream infections in Blantyre, Malawi: a prospective cohort study

The burden of antimicrobial resistance is a major threat to global health; however, prospective clinical outcome data from Africa are scarce. In Malawi, third-generation cephalosporins are the antibiotics of choice in patients admitted to hospital despite a rapid proliferation of resistance to these drugs. We aimed to quantify the effect of resistance to third-generation cephalosporins on mortality and length of hospital stay among patients with bloodstream infections. We did a prospective cohort study of patients admitted to Queen Elizabeth Central Hospital in Blantyre, Malawi. Patients of all ages who had positive blood cultures for Enterobacterales were included, with the exception of those from the genus Salmonella, and were followed up for 180 days. We characterised blood culture isolates using whole-genome sequencing and used Cox regression models to estimate the effect of resistance to third-generation cephalosporins on length of hospital stay, in-hospital mortality, and survival. Between Jan 31, 2018, and Jan 13, 2020, we recruited 326 patients, from whom 220 (68%) of 326 isolates were resistant to third-generation cephalosporins. The case fatality proportion was 45% (99 of 220) in patients with bloodstream infections that were resistant to third-generation cephalosporins, and 34% (36 of 106) in patients with bloodstream infections that were sensitive to third-generation cephalosporins. Resistance to third-generation cephalosporins was associated with an increased probability of in-hospital mortality (hazard ratio [HR] 1·44, 95% CI 1·02-2·04), longer hospital stays (1·5 days, 1·0-2·0) and decreased probability of discharge alive (HR 0·31, 0·22-0·45). Whole-genome sequencing showed a high diversity of sequence types of both Escherichia coli and Klebsiella pneumoniae. Although isolates associated with death were distributed across clades, we identified three E coli clades (ST410, ST617, and ST648) that were isolated from 14 patients who all died. Resistance to third-generation cephalosporins is associated with increased mortality and longer hospital stays in patients with bloodstream infections in Malawi. These data show the urgent need for allocation of resources towards antimicrobial resistance mitigation strategies in Africa. Wellcome Trust and Wellcome Asia and Africa Programme.

Children with malignancies and septic shock - an attempt to understand the risk factors

ObjectivesTo explain the high mortality of septic shock in children with cancer. MethodsA retrospective cohort from 2016 to 2020, of children aged 0 to 18 years, and septic shock. ResultsThe authors included 139 patients. Acute lymphocytic leukemia was the most frequent diagnosis (16.5%), and Gram-negative bacteria were the most frequent blood culture isolates (22.3%). There were 57 deaths in ICU (41%), 10 in the first 24 hours of shock (early death). A LASSO model with variables: neutropenia (coefficient 0.215), respiratory (0.81), hematological (1.41), and neurological (0.72) dysfunctions, age (-0.002) and solid tumor recurrence (0.34) generated AUC = 0.79 for the early death outcome. Survivors had significant differences in the PRISM-IV score (mean ± SD 10.9 ± 6.2 in the survivors, 14.1 ± 6.5 in the deceased, p = 0.004), and in the mean number of organ dysfunctions (3.2 ± 1.1 in the survivors, 3.8 ± 6.5 in the deceased, p < 0.001). A positive fluid balance in the first 24 hours of sepsis between 2% and 6% of body weight showed a reduction effect on the probability of death in ICU (hazard ratio 0.47, 95% CI 0.24-0.92, p = 0.027). The recurrence of any cancer was a predictor of in-hospital death, regardless of severity. ConclusionsRecurrence of any cancer is an important risk of sepsis-related death. A positive fluid balance between 20 and 60 mL/kg or 2% and 6% of body weight in the first 24 hours after the onset of sepsis is related to lower mortality.