Haemophilus influenzae blood-stream infection and third-generation cephalosporin susceptibility testing: a comparative case study using EUCAST and CLSI guidelines.

Introduction: In this comparative case study, we discuss clinically relevant discrepancies of antimicrobial susceptibility testing (AST) interpretation for ceftriaxone against a non-typable, beta-lactamase negative, ampicillin-resistant (BLNAR) Haemophilus influenzae isolated from a blood culture. Case report: A 74-year-old man presented with a 3 day illness characterized by shortness of breath and dry cough, and was noted to be febrile and hypoxic on admission. A blood culture bottle flagged positive with Gram-negative coccobacilli, later identified as Haemophilus influenzae with the patient commenced on ceftriaxone. The isolate was beta-lactamase negative and antibiotic susceptibility testing (AST) using disc diffusion revealed the isolate resistant to ceftriaxone and ampicillin by EUCAST methodology, with the patient subsequently changed to amoxicillin/clavulanate. Further AST using the CLSI methodology in parallel demonstrated discrepant results between the two susceptibility methods. The patient recovered without complications. Conclusion: This discrepancy could lead to inconsistent reporting of susceptibilities between laboratories, and consequently antibiotic prescribing, especially for invasive isolates. As more laboratories adopt EUCAST methodologies for AST interpretation in Australia and globally, it is important for clinicians to consider the clinical implications of these methodological discrepancies.

Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?

IMPORTANCE: Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.

Antibiotic Prescribing and Antimicrobial Resistance from an Australian Perspective.

In Australia, the overuse or inappropriate prescribing of antimicrobials in health (human and animal) and agriculture is a concern that has increased over the years. This has given bacteria, fungi, parasites, and some viruses through exposure more opportunity to develop resistance. A process of artificial and natural selection, which favors microorganisms in developing the strongest natural defenses increasing prevalence of antimicrobial resistance (AMR). Appropriate use of antimicrobials can be lifesaving to humans and animals, but inappropriate use needs to be closely monitored and acted on to promote improved safety and quality of care. Inappropriate use includes prescribing antimicrobials when they are not necessary, prescribing the wrong type of antimicrobial and prescribing them for the incorrect duration. This short report reviews and summarizes some of the efforts used in Australia to control AMR and antibiotic prescribing.

Success of ceftazidime-avibactam and aztreonam in combination for a refractory biliary infection with recurrent bacteraemia due to blaIMP-4 carbapenemase-producing Enterobacter hormaechei subsp. oharae.

BACKGROUND: Infections due to metallo-beta-lactamase (MBL)-producing organisms are becoming a significant problem, and antibiotic treatment options are limited. Aztreonam inhibits MBLs, and its use in combination with ceftazidime-avibactam (CAZ-AVI-AZT) to inhibit other beta-lactamases shows promise. METHODS: A 45-year-old woman suffered from recurrent and sustained MBL (blaIMP-4)+ Enterobacter cloacae complex bacteraemia from an undrainable biliary source, and had failed nine alternative antibiotic regimens over a 5-month period. The 10th episode was successfully treated with CAZ-AVI-AZT, and she has had no further relapses. Three of the isolates underwent whole-genome sequencing (WGS) on the MiSeq platform and were analysed with the Nullarbor pipeline. RESULTS: A layered Etest method for synergy between CAZ-AVI and aztreonam demonstrated an MIC of 2 mg l-1 for the combination. Isolates were identified by WGS as Enterobacter hormaechei subsp. oharae . All three of the isolates had blaTEM-4 ESBL, blaOXA-1 and blaACT-25. Two of the carbapenem-resistant isolates contained blaIMP-4. CONCLUSION: While aztreonam inhibits MBLs, MBL-positive isolates often express other beta-lactamase enzymes. Avibactam inhibits ESBLs and other beta-lactamases, and its use in this case possibly contributed to therapeutic success due to inhibition of the concomitant blaTEM-4 in the isolates. This case demonstrates that phenotypic antimicrobial susceptibility testing (layered Etests for synergy), backed up by WGS, can produce results that allow tailored antimicrobial therapy in difficult infections. This case adds to the evidence for using CAZ-AVI-AZT in serious MBL infections.

Wound infection caused by Neisseria zoodegmatis, a zoonotic pathogen: a case report.

The isolation of Neisseria zoodegmatis from a 63-year-old female presenting to the emergency department following a cat bite injury to her right hand is described in this report. N. zoodegmatis , also known as Centers for Disease Control (CDC) group EF-4b, is considered to be a zoonotic pathogen, and is usually associated with dog or cat bites. Despite the potential of this organism to cause serious soft tissue infections, it can be overlooked in routine clinical laboratories due to its slow growth characteristics and when the history of animal bite is not provided to the laboratory. This case highlights the importance of appropriate clinical history provision to the microbiology laboratory to help provide important information about potential pathogens and allow microbiologists to optimize culture and identification methods. The introduction of tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) into clinical laboratories allows identification and the interpretation of results to be performed within a few minutes of isolation on proper culture media, as opposed to traditional methods, whose slowness may be problematic, as shown in this case report.

Identification and characterisation of fosfomycin resistance in Escherichia coli urinary tract infection isolates from Australia.

Of 1033 Escherichia coli urinary tract infection isolates collected from females >12 years of age in Australia in 2019, only 2 isolates were resistant to fosfomycin with a minimum inhibitory concentration (MIC) of >256 mg/L. Despite having different multilocus sequence types, the two isolates harboured an identical plasmid-encoded fosA4 gene. The fosA4 gene has previously been identified in a single clinical E. coli isolate cultured in Japan in 2014. Each fosfomycin-resistant isolate harboured two conjugative plasmids that possessed an array of genes conferring resistance to aminoglycosides, ß-lactams, macrolides, quinolones, sulfonamides and/or trimethoprim.

Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex.

The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum ß-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.

Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital.

This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried blaCTX -M-gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII-IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids.

IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.

Long-term survival of implantable cardioverter defibrillator recipients with end-stage renal disease.

BACKGROUND: The efficacy of implantable cardioverter-defibrillators (ICD) for primary prevention of sudden cardiac death (SCD) has not been studied in patients with end-stage renal disease (ESRD) and left ventricular dysfunction. We sought to identify predictors of long-term survival among ICD recipients with and without ESRD. METHODS: Patients implanted with an ICD at our institution from January 2006 to March 2014 were retrospectively identified. Clinical and demographic characteristics were collected. Patients were stratified by the presence of ESRD at the time of ICD implant. Mortality data were collected from the Social Security Death Index (SSDI). RESULTS: A total of 3453 patients received an ICD at our institution in the pre-specified time period, 184 (5.3%) of whom had ESRD. In general, ESRD patients were sicker and had more comorbidities. Kaplan Meier survival curve showed that ESRD patients had worse survival as compared with non-dialysis patients (p<0.001). Following adjustment for differences in baseline characteristics, patients with ESRD remained at increased long-term mortality in the Cox model. The one-year mortality in the ESRD patients was 18.1%, as compared with 7.7% in the non-dialysis cohort (p<0.001). The three-year mortality in ESRD patients was 43%, as compared with 21% in the non-dialysis cohort (p<0.001). CONCLUSION: ESRD patients are at significantly increased risk of mortality as compared with a non-dialysis cohort. While the majority of these patients survive more than one year post-diagnosis, the three-year mortality is high (43%). Randomized studies addressing the benefits of ICDs in ESRD patients are needed to better define their value for primary prevention of SCD.

Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.

Carbapenem-resistant Enterobacteriaceae (CRE) are a pressing public health issue due to limited therapeutic options to treat such infections. CREs have been predominantly isolated from humans and environmental samples and they are rarely reported among companion animals. In this study we report on the isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from a companion animal. Carbapenemase-producing S. enterica Typhimurium carrying blaIMP-4 was identified from a systemically unwell (index) cat and three additional cats at an animal shelter. All isolates were identical and belonged to ST19. Genome sequencing revealed the acquisition of a multidrug-resistant IncHI2 plasmid (pIMP4-SEM1) that encoded resistance to nine antimicrobial classes including carbapenems and carried the blaIMP-4-qacG-aacA4-catB3 cassette array. The plasmid also encoded resistance to arsenic (MIC-150 mM). Comparative analysis revealed that the plasmid pIMP4-SEM1 showed greatest similarity to two blaIMP-8 carrying IncHI2 plasmids from Enterobacter spp. isolated from humans in China. This is the first report of CRE carrying a blaIMP-4 gene causing a clinical infection in a companion animal, with presumed nosocomial spread. This study illustrates the broader community risk entailed in escalating CRE transmission within a zoonotic species such as Salmonella, and in a cycle that encompasses humans, animals and the environment.

Management of New-Onset Postoperative Atrial Fibrillation Utilizing Insertable Cardiac Monitor Technology to Observe Recurrence of AF (MONITOR-AF).

BACKGROUND: New-onset postoperative atrial fibrillation (POAF) occurs in up to 30% of patients undergoing coronary artery bypass grafting (CABG). POAF is associated with short- and long-term mortality. METHODS: To identify the true incidence and time course of recurrent atrial fibrillation (AF) in patients with POAF, we prospectively assigned 23 patients with POAF to receive an implantable loop recorder (ILR; Medtronic Inc., Minneapolis, MN, USA) for the detection of recurrent AF. Two electrophysiologists independently adjudicated monthly ILR transmissions to classify recurrent AF. We defined AF as any episode lasting ≥6 minutes. RESULTS: The cohort included 23 subjects averaging 69.1 ± 7.2 years of age. Their mean CHADS2 score averaged 1.9 ± 0.8. Note that 26.1% underwent direct current cardioversion prior to discharge; 95.7% left the hospital taking amiodarone and 26.1% warfarin. A total of 14 patients (60.9%) experienced recurrent AF. AF first recurred within 3 months in nine patients (39.1%), and in 10 patients AF emerged or continued beyond 3 months. Eight of 17 (47.1%) patients followed for at least 1 year experienced AF recurrence beyond 1 year of CABG. The time from surgery to first AF episode averaged 143 ± 22.5 days. Long-term monitoring shows that 60.9% of patients with POAF develop recurrent AF. CONCLUSION: POAF may represent a propensity for recurrent paroxysmal atrial fibrillation, and not simply a transient consequence of postoperative stress and inflammation. Better detection of recurrent AF might identify patients at risk for stroke who would benefit from continuing anticoagulation.

High-risk patients with inoperative aortic stenosis: use of transapical, transaortic, and transcarotid techniques.

BACKGROUND: Patient characteristics and procedural outcomes from nontransfemoral (non-TF) transcatheter aortic valve replacement (TAVR) in high-risk or inoperable patients with aortic stenosis have been incompletely reported. The purpose of this study was to compare outcomes with non-TF TAVR access techniques including transapical (TA), transaortic (TAo), and transcarotid (TC) TAVR with a balloon-expandable valve. METHODS: A retrospective review was performed of all patients undergoing TA, TAo, and TC TAVR from 2007 to 2013 at Emory University. Preoperative risk factors and postoperative outcomes were evaluated using Valve Academic Research Consortium-2 definitions. RESULTS: Of 469 patients undergoing TAVR during that period at our institution, 139 underwent TA TAVR, 35 had Tao TAVR, and 11 had TC TAVR. Patients undergoing TC TAVR were younger than those undergoing TA TAVR and TAo TAVR (mean ages: TC, 68.9 ± 23.6 years; TA, 81.3 ± 7.7 years; Tao, 83.8 ± 8.3 years; p = 0.017). Most patients undergoing TAo TAVR were women (82.9%), whereas patients undergoing TA TAVR were more likely to be men (62.6%). Slightly more than half of patients undergoing TA TAVR (54.7%) and TC (54.6%) TAVR had undergone previous coronary artery bypass grafting (CABG), whereas no patients underwent TAo TAVR (0%). There was no preoperative difference in ejection fraction, New York Heart Association classification, significant chronic obstructive pulmonary disease, and The Society of Thoracic Surgeons predicted risk of mortality between TA TAVR, Tao TAVR, and TC TAVR, respectively. Average postoperative length of stay was 9 to 11 days and was similar among groups (p = 0.22). There were 13 (9.4%) TA TAVR operative deaths and 4 (11.4%) operative deaths in the TAo TAVR group. There were no deaths in the TC TAVR group. CONCLUSIONS: In high-risk and inoperable patients who are not candidates for TF TAVR, careful selection of alternative access options can lead to excellent and comparable postoperative outcomes.

Transcatheter aortic valve replacement has improved short-term but similar midterm outcomes in isolated aortic valve replacement after prior coronary artery bypass grafting.

BACKGROUND: An increasing number of patients with prior coronary artery bypass grafting (CABG) now present with severe aortic stenosis. The proposed benefit of surgical (SAVR) vs transcatheter aortic valve replacement (TAVR) is unknown. The objective of this study was to compare short-term and midterm outcomes of patients undergoing isolated SAVR vs TAVR in those with prior CABG. METHODS: A retrospective analysis was performed of 255 patients who underwent isolated SAVR after prior CABG from January 2002 to February 2013 at Emory University. Outcomes of 148 patients undergoing SAVR (2002 to 2013) and 107 undergoing TAVR (2007 to 2013) were compared using multivariable logistic regression and analysis of variance techniques, adjusting for The Society of Thoracic Surgeons (STS) risk score. Kaplan-Meier plots were used to determine survival rates, and midterm survival between groups was compared using the Cox proportional hazards model. RESULTS: TAVR patients were older (79.8 ± 7.9 years vs 72.5 ± 8.8 years, p < 0.001) but were gender equivalent (female: 24% vs 22%, p = 0.61). The preoperative ejection fraction was similar between groups (TAVR: 0.433 ± 0.131 vs SAVR: 0.469 ± 0.148%, p = 0.60). The TAVR group had a significantly higher the STS risk scores (11.8% vs 7.1%, p < 0.001). All-cause 30-day mortality was 1.9% for TAVR and 4.1% for SAVR (p = 0.32), a result that marginally favors TAVR after risk adjustment (adjusted odds ratio, 0.19; p = 0.07). Postoperative morbidity and resource utilization was significantly higher in the SAVR patients. Midterm survival was similar between the two groups after adjustment (adjusted hazard ratio, 0.78, p = 0.46). CONCLUSIONS: Excellent outcomes can be achieved in SAVR or TAVR after prior CABG. Although TAVR improves short-term outcomes and resource utilization compared with SAVR, midterm mortality outcomes are similar.