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Infection Control and Hospital... Mar 2024We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting.
OBJECTIVE
We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting.
METHODS
During 2017-2019, 592 patient-room sinks were sampled in 34 departments. Patient weekly rectal swab CPE surveillance was universally performed. Repeated sink sampling was conducted in 9 departments. Isolates from patients and sinks were characterized using pulsed-field gel electrophoresis (PFGE), and pairs of high resemblance were sequenced by Oxford Nanopore and Illumina. Hybrid assembly was used to fully assemble plasmids, which are shared between paired isolates.
RESULTS
In total, 144 (24%) of 592 CPE-contaminated sinks were detected in 25 of 34 departments. Repeated sampling (n = 7,123) revealed that 52%-100% were contaminated at least once during the sampling period. Persistent contamination for >1 year by a dominant strain was common. During the study period, 318 patients acquired CPE. The most common species were , , and spp. In 127 (40%) patients, a contaminated sink was the suspected source of CPE acquisition. For 20 cases with an identical sink-patient strain, temporal relation suggested sink-to-patient transmission. Hybrid assembly of specific sink-patient isolates revealed that shared plasmids were structurally identical, and SNP differences between shared pairs, along with signatures for potential recombination events, suggests recent sharing of the plasmids.
CONCLUSIONS
CPE-contaminated sinks are an important source of transmission to patients. Although traditionally person-to-person transmission has been considered the main route of CPE transmission, these data suggest a change in paradigm that may influence strategies of preventing CPE dissemination.
Topics: Humans; Carbapenem-Resistant Enterobacteriaceae; Enterobacteriaceae; beta-Lactamases; Bacterial Proteins; Klebsiella pneumoniae; Escherichia coli; Enterobacteriaceae Infections
PubMed: 38149351
DOI: 10.1017/ice.2023.270 -
Journal of Global Antimicrobial... Mar 2024Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially...
OBJECTIVES
Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially prone to acquire resistance genes such as those encoding extended-spectrum beta-lactamases (ESBLs) and carbapenemases.
METHODS
Cloacal samples (n = 206) of free-living feral pigeons (C. livia) were collected in Sousse and Monastir, Tunisia. Antimicrobial susceptibility profiles were determined by disc-diffusion, and resistant isolates were short- and long-read whole-genome sequenced. Sequence analysis was performed using tools of the Centre for Genomic Epidemiology, and Phylogenetic analysis was performed based on the core-genome MLST.
RESULTS
Fourteen (14/206, 6.8%) pigeons harboured Enterobacterales resistant to last-generations cephalosporins, of which 10 were CTX-M-15- or CTX-M-27-producers, while two (1.0%) carried a VIM-2-producing Pseudomonas putida. Positive pigeons lived on four different livestock farms. Three STs (ST206, ST5584, ST8149) were identified among E. coli, of which ST5584 and ST8149 were found in two different farms. Genetic diversity was also observed in Enterobacter cloacae and P. putida isolates. The bla genes were chromosomally encoded, while the bla genes were carried on highly similar IncF/F-:A-:B53 plasmids. The bla gene was located on a class 1 integron co-harbouring several resistance genes.
CONCLUSION
Pigeons living on livestock farms carried clinically important resistance genes encoding ESBLs and carbapenemases. Our results evidenced that both clonal (ST8149 and ST5584) and plasmidic (IncF/F-:A-:B53) transfers played a role in the spread of resistance genes among pigeons. Further studies are needed to identify factors favouring the transfer and persistence of resistance genes within the pigeon communities.
Topics: Animals; Humans; Columbidae; Escherichia coli; Pseudomonas putida; Multilocus Sequence Typing; Tunisia; Phylogeny; beta-Lactamases; Anti-Infective Agents
PubMed: 38145799
DOI: 10.1016/j.jgar.2023.12.013 -
Pediatric Research Apr 2024The mechanism underlying anorectal malformations (ARMs)-related VACTERL (vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, and renal and limb... (Review)
Review
The mechanism underlying anorectal malformations (ARMs)-related VACTERL (vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, and renal and limb abnormalities) remains unclear. Copy number variation (CNV) contributed to VACTERL pathogenicity. Here, we report a novel CNV in 8p23 and 12q23.1 identified in a case of ARMs-related VACTERL association. This 12-year-old girl presented a cloaca (urethra, vagina, and rectum opening together and sharing a single tube length), an isolated kidney, and a perpetuation of the left superior vena cava at birth. Her intelligence, growth, and development were slightly lower than those of normal children of the same age. Array comparative genomic hybridization revealed a 9.6-Mb deletion in 8p23.1-23.3 and a 0.52-Mb duplication in 12q23.1 in her genome. Furthermore, we reviewed the cases involving CNVs in patients with VACTERL, 8p23 deletion, and 12q23.1 duplication, and our case was the first displaying ARMs-related VACTERL association with CNV in 8p23 and 12q23.1. These findings enriched our understanding between VACTERL association and the mutations of 8p23 deletion and 12q23.1 duplication. IMPACT: This is a novel case of a Chinese girl with anorectal malformations (ARMs)-related VACTERL with an 8p23.1-23.3 deletion and 12q23.1 duplication. Cloaca malformation is presented with novel copy number variation in 8p23.1-23.3 deletion and 12q23.1 duplication.
Topics: Humans; Female; Limb Deformities, Congenital; Anal Canal; Child; Spine; Esophagus; DNA Copy Number Variations; Trachea; Heart Defects, Congenital; Chromosomes, Human, Pair 8; Chromosomes, Human, Pair 12; Genetic Association Studies; Mutation; Comparative Genomic Hybridization; Kidney; Cloaca; Phenotype; Abnormalities, Multiple
PubMed: 38135728
DOI: 10.1038/s41390-023-02928-0 -
International Microbiology : the... Dec 2023Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed...
Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.
PubMed: 38044418
DOI: 10.1007/s10123-023-00461-y -
Antimicrobial Agents and Chemotherapy Dec 2023Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant , but carbapenem resistance due to acquisition of...
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant , but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. carbapenemase () is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn transposon. This means that alongside clonal expansion, can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular -encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian -encoding plasmids. We further estimated the genomic location of incomplete -encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of genomic loci and indicate that multiple, distinct plasmid clusters have contributed to spread and persistence in Canada.
Topics: Humans; Canada; beta-Lactamases; Plasmids; Bacterial Proteins; Klebsiella pneumoniae; Anti-Bacterial Agents; Carbapenems; Genomics; Klebsiella Infections; Microbial Sensitivity Tests
PubMed: 37971242
DOI: 10.1128/aac.00860-23 -
Archives of Orthopaedic and Trauma... Nov 2023While gram negative (GN) periprosthetic joint infections (PJI) have previously been described as difficult to treat pathogens with high rates of reinfection, limited...
PURPOSE
While gram negative (GN) periprosthetic joint infections (PJI) have previously been described as difficult to treat pathogens with high rates of reinfection, limited investigations have addressed midterm outcomes and risk of infection persistence by the same pathogen. This study analyzed (1) baseline demographics, treatment strategy, and midterm outcomes of GN PJIs, as well as (2) differences in reinfection and relapse rates compared to gram positive (GP) PJIs.
METHODS
We identified 29 patients that were revised for 30 GN PJIs of total hip arthroplasties (THAs) between 2010 and 2020 using a university-based hip registry. Mean age was 77 years, 63% were females (19), and mean BMI was 27 kg/m. Major causative pathogens included Escherichia coli (12), Klebsiella pneumoniae (5), Pseudomonas aeruginosa (5), and Enterobacter cloacae complex (5). Mean follow-up was 3.5 years. Study outcomes included (1) Kaplan-Meier survivorship analyses of all 30 GN PJIs, and (2) comparison of 18 two-stage exchanges for GN PJIs and 104 two-stage exchanges for GP PJIs, performed during the time from 2013 to 2017.
RESULTS
(1) The 5-year survivorship free of recurrent PJI was 69%, and there were 7 recurrent PJIs at a mean of 2 years. There were 2 further suprafascial wound infections, resulting in a 61% survivorship free of any infection at 5-years. At a mean of 2 years, there were 7 patients with reinfection by the same GN pathogen (6 PJIs, one wound infection) as at index revision (23%). (2) Following two-stage exchange, the 5-year survivorship free of recurrent PJI (GN: 74%; GP: 91%; p = 0.072), any infection (GN: 61%; GP: 91%; p = 0.001), and reinfection by the same pathogen was significantly lower among GN PJIs (GN: 73%; GP: 98%; p < 0.001).
CONCLUSIONS
Patients revised for GN PJIs are at increased risk of reinfection as opposed to GP infections. Affected patients must be counseled on the exceptionally high risk of infection persistence with one in four developing relapses.
LEVEL OF EVIDENCE
Therapeutic Level III.
PubMed: 37910220
DOI: 10.1007/s00402-023-05104-5 -
Journal of Infection and Public Health Dec 2023We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions...
BACKGROUND
We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana.
METHODS
Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome.
RESULTS
We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants.
CONCLUSIONS
Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
Topics: Humans; Carbapenems; Anti-Bacterial Agents; Multilocus Sequence Typing; Plasmids; Klebsiella pneumoniae; beta-Lactamases; Escherichia coli; Microbial Sensitivity Tests; Klebsiella Infections
PubMed: 37866269
DOI: 10.1016/j.jiph.2023.10.013 -
Surgery Open Science Dec 2023Ventilator-associated pneumonias (VAPs) are a complication of mechanical ventilation in the intensive care unit (ICU) that increase length of stay, morbidity, and...
INTRODUCTION
Ventilator-associated pneumonias (VAPs) are a complication of mechanical ventilation in the intensive care unit (ICU) that increase length of stay, morbidity, and mortality. While identifying and treating infections early is paramount to improving patient outcomes, more and more data demonstrate limited courses of antibiotics improve outcomes. Prolonged (10-14 day) courses of antibiotics have remained the standard of care for pneumonia due to gram-negative bacilli (GNR). We aimed to review our GNR VAPs to assess risk factors for recurrent GNR infections.
METHODS
We reviewed trauma patients who developed VAP from 02/2019 through 05/2022. Demographics, injury characteristics, and outcomes were reviewed with a focus on pneumonia details including the cultured pathogen(s), antibiotic(s) used, treatment duration, and presence of recurrent infections. We then compared single episode VAPs to multiple episode VAPs among patients infected by GNRs.
RESULTS
Eleven of the fifty trauma patients admitted to the ICU suffered a VAP caused by a GNR. Of these eleven patients, six experienced a recurrent infection, four of which were caused by and two of which were caused by . Among the patients who received ten days of antibiotic treatment, half suffered a recurrence. Although, there was no difference in the microbiology or antibiotic duration between the recurrences and single episodes.
CONCLUSION
Despite prolonged use of antibiotics, we found that the risk of recurrent or persistent infections was high among patients with VAP due to GNB. Further study is needed to determine optimal treatment to minimize the risk of these recurrences.
KEY MESSAGE
Ventilator-associated pneumonia due to gram-negative bacilli is a rare but high morbidity complication in intensive care units. Despite prolonged duration of therapy, these infections still appear to account for many recurrent infections and further study into optimal therapy is warranted.
PubMed: 37789948
DOI: 10.1016/j.sopen.2023.09.014 -
Nature Communications Sep 2023The selective enzymatic reduction of nitroaliphatic and nitroaromatic compounds to aliphatic amines and amino-, azoxy- and azo-aromatics, respectively, remains a...
The selective enzymatic reduction of nitroaliphatic and nitroaromatic compounds to aliphatic amines and amino-, azoxy- and azo-aromatics, respectively, remains a persisting challenge for biocatalysis. Here we demonstrate the light-powered, selective photoenzymatic synthesis of aliphatic amines and amino-, azoxy- and azo-aromatics from the corresponding nitro compounds. The nitroreductase from Bacillus amyloliquefaciens, in synergy with a photocatalytic system based on chlorophyll, promotes selective conversions of electronically-diverse nitroarenes into a series of aromatic amino, azoxy and azo products with excellent yield (up to 97%). The exploitation of an alternative nitroreductase from Enterobacter cloacae enables the tailoring of a photoenzymatic system for the challenging synthesis of aliphatic amines from nitroalkenes and nitroalkanes (up to 90% yield). This photoenzymatic reduction overcomes the competing bio-Nef reaction, typically hindering the complete enzymatic reduction of nitroaliphatics. The results highlight the usefulness of nitroreductases to create selective photoenzymatic systems for the synthesis of precious chemicals, and the effectiveness of chlorophyll as an innocuous photocatalyst, enabling the use of sunlight to drive the photobiocatalytic reactions.
Topics: Nitro Compounds; Amines; Alkanes; Alkenes; Chlorophyll
PubMed: 37673927
DOI: 10.1038/s41467-023-41194-w -
Croatian Medical Journal Aug 2023Bloodstream infections (BSI) are frequently encountered during extracorporeal membrane oxygenation (ECMO) support. Once septicemia is observed, treatment should be...
Bloodstream infections (BSI) are frequently encountered during extracorporeal membrane oxygenation (ECMO) support. Once septicemia is observed, treatment should be rapid, adequate, and multifaceted, particularly in advanced ECMO configurations. We report on a case of a 60-year-old male patient with acute-on-chronic heart failure due to ischemic cardiomyopathy. The treatment was complicated by cardiogenic shock requiring veno-arterial ECMO support, and, due to persistent pulmonary congestion, an upgrade with an additional left-atrial drainage cannula. After seven days of ECMO support, septicemia with shock ensued. Ex iuvantibus antibiotic treatment was started promptly. We wanted to minimize the likelihood of bacterial biofilm build-up requiring an exchange of the ECMO circuit and cannula, which was expected to be challenging. Therefore, we added a Seraph-100 Microbind affinity blood filter (providing blood purification with the potential for rapid bacterial clearance) to the ECMO circuit. Initial blood cultures tested positive for Enterobacter cloacae. Following a course of Seraph-100 treatment, bacteremia, septicemia, and shock resolved. There was no need for a circuit or cannula exchange. The additional eleven days of ECMO support were uneventful. The patient was successfully bridged to long-term mechanical circulatory support. We believe that the synergistic effect of early implementation of both broad-spectrum antibiotic treatment and blood purification with the potential for rapid bacterial clearance (such as the one provided with the Seraph-100 Microbind affinity blood filter) is crucial in BSI in patients receiving advanced ECMO.
Topics: Male; Humans; Middle Aged; Extracorporeal Membrane Oxygenation; Enterobacter cloacae; Cannula; Sepsis; Bacteremia
PubMed: 37654040
DOI: 10.3325/cmj.2023.64.284