A panel of diverse Klebsiella pneumoniae clinical isolates for research and development.

Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum ß-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.

Infection preventionist staffing levels and rates of 10 types of healthcare-associated infections: A 9-year ambidirectional observation.

OBJECTIVE: To quantitatively evaluate relationships between infection preventionists (IPs) staffing levels, nursing hours, and rates of 10 types of healthcare-associated infections (HAIs). DESIGN AND SETTING: An ambidirectional observation in a 528-bed teaching hospital. PATIENTS: All inpatients from July 1, 2012, to February 1, 2021. METHODS: Standardized US National Health Safety Network (NHSN) definitions were used for HAIs. Staffing levels were measured in full-time equivalents (FTE) for IPs and total monthly hours worked for nurses. A time-trend analysis using control charts, t tests, Poisson tests, and regression analysis was performed using Minitab and R computing programs on rates and standardized infection ratios (SIRs) of 10 types of HAIs. An additional analysis was performed on 3 stratifications: critically low (2-3 FTE), below recommended IP levels (4-6 FTE), and at recommended IP levels (7-8 FTE). RESULTS: The observation covered 1.6 million patient days of surveillance. IP staffing levels fluctuated from ≤2 IP FTE (critically low) to 7-8 IP FTE (recommended levels). Periods of highest catheter-associated urinary tract infection SIRs, hospital-onset Clostridioides difficile and carbapenem-resistant Enterobacteriaceae infection rates, along with 4 of 5 types of surgical site SIRs coincided with the periods of lowest IP staffing levels and the absence of certified IPs and a healthcare epidemiologist. Central-line-associated bloodstream infections increased amid lower nursing levels despite the increased presence of an IP and a hospital epidemiologist. CONCLUSIONS: Of 10 HAIs, 8 had highest incidences during periods of lowest IP staffing and experience. Some HAI rates varied inversely with levels of IP staffing and experience and others appeared to be more influenced by nursing levels or other confounders.

A cluster-control approach to a coronavirus disease 2019 (COVID-19) outbreak on a stroke ward with infection control considerations for dementia and vascular units.

OBJECTIVE: We sought to contain a healthcare-associated coronavirus disease 2019 (COVID-19) outbreak, to evaluate contributory factors, and to prevent future outbreaks. DESIGN: Quasi-experimental cluster-control outbreak evaluation. METHODS: All patients and staff on the outbreak ward (case cluster), and randomly selected patients and staff on COVID-19 wards (positive control cluster) and a non-COVID-19 wards (negative control cluster) underwent reverse-transcriptase polymerase chain reaction (RT-PCR) testing. Hand hygiene and personal protective equipment (PPE) compliance, detection of environmental SARS-COV-2 RNA, patient behavior, and SARS-CoV-2 IgG antibody prevalence were assessed. RESULTS: In total, 145 staff and 26 patients were exposed, resulting in 24 secondary cases. Also, 4 of 14 (29%) staff and 7 of 10 (70%) patients were asymptomatic or presymptomatic. There was no difference in mean cycle threshold between asymptomatic or presymptomatic versus symptomatic individuals. None of 32 randomly selected staff from the control wards tested positive. Environmental RNA detection levels were higher on the COVID-19 ward than on the negative control ward (OR, 19.98; 95% CI, 2.63-906.38; P < .001). RNA levels on the COVID-19 ward (where there were no outbreaks) and the outbreak ward were similar (OR, 2.38; P = .18). Mean monthly hand hygiene compliance, based on 20,146 observations (over preceding year), was lower on the outbreak ward (P < .006). Compared to both control wards, the proportion of staff with detectable antibodies was higher on the outbreak ward (OR, 3.78; 95% CI, 1.01-14.25; P = .008). CONCLUSION: Staff seroconversion was more likely during a short-term outbreak than from sustained duty on a COVID-19 ward. Environmental contamination and PPE use were similar on the outbreak and control wards. Patient noncompliance, decreased hand hygiene, and asymptomatic or presymptomatic transmission were more frequent on the outbreak ward.

Severe recurrent Streptobacillus moniliformis endocarditis in a pregnant woman, and review of the literature.

BACKGROUND: Rat bite fever is a systemic febrile illness caused by infection with the Gram-negative bacillus Streptobacillus moniliformis following a bite, scratch, or contact with excrement. Only 26 cases of native valve endocarditis have been reported to date. We could find no other reports of severe Streptobacillus endocarditis requiring valve replacement in a young, pregnant patient. CASE PRESENTATION: A pregnant patient sought care for right leg pain, fevers, left upper quadrant pain, generalized weakness, fatigue, and inability to bear weight on her right leg. She had a syncopal episode 9 months earlier, resulting in a mandibular fracture and internal fixation hardware. Her pregnancy was complicated by hyperemesis and weight loss. Her pets included a rescued wild bird, a cat, and four rats. Her parents rescued stray cats, and she recalled multiple cat bites and scratches since childhood. She denied injection drug use. Ultrasound indicated a right popliteal artery thrombus. Transesophageal echocardiogram revealed a 2 cm × 0.7 cm vegetation. Angiography demonstrated multiple splenic infarcts and bilateral renal infarcts. She underwent mitral valve repair. The mitral valve Gram stain demonstrated 2+ Gram-negative rods, rare Gram-positive rods, and moderate white blood cells. Propionibacterium spp. was isolated from the mitral valve tissue on Columbia agar incubated anaerobically. Anaerobic and aerobic cultures of the valve tissue on all other broths and agars remained negative at 14 days. Hematoxylin and eosin stains showed a fibro-inflammatory vegetation. Aggregates of rod-shaped bacteria were identified on Warthin Starry/Steiner stain. Bartonella titers were positive for B. henselae IgG 1:256, IgM < 1:20. Brown-Hopps Gram stain, AFB, and GMS stains for bacterial and fungal microorganisms were negative. Broad range bacterial PCR and sequencing of a segment of 16 s rRNA gene of the valve tissue matched to Streptobacillus sp. (genus level) and most closely related to Streptobacillus moniliformis. CONCLUSION: This case demonstrates diagnostic and therapeutic challenges associated with a relatively uncommon cause of endocarditis. The diagnosis of rat bite fever was delayed due to symptoms of a concomitant pregnancy. Other confounders included possible alternative sources or co-infections with another zoonosis from multiple pets, and an odontogenic source due to presence of exposed jaw hardware.

A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development.

Over the past two decades, Acinetobacter baumannii has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant A. baumannii as a priority 1 (critical) pathogen for research and development of new antibiotics. A key component in supporting this effort is accessibility to diverse and clinically relevant strains for testing. Here, we describe a panel of 100 diverse A. baumannii strains for use in this endeavor. Whole-genome sequencing was performed on 3,505 A. baumannii isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. Isolates were cultured from clinical samples at health care facilities around the world between 2001 and 2017. Core-genome multilocus sequence typing and high-resolution single nucleotide polymorphism (SNP)-based phylogenetic analyses were used to select a final panel of 100 strains that captured the genetic diversity of the collection. Comprehensive antibiotic susceptibility testing was also performed on all 100 isolates using 14 clinically relevant antibiotics. The final 100-strain diversity panel contained representative strains from 70 different traditional Pasteur scheme multilocus sequence types, including major epidemic clones. This diversity was also reflected in antibiotic susceptibility and antimicrobial resistance (AMR) gene content, with phenotypes ranging from pansensitive to panresistant, and over 100 distinct AMR gene alleles identified from 32 gene families. This panel provides the most diverse and comprehensive set of A. baumannii strains for use in developing solutions for combating antibiotic resistance. The panel and all available metadata, including genome sequences, will be available to industry and academic institutions and federal and other laboratories free of charge.

Sustainably reducing device utilization and device-related infections with DeCATHlons, device alternatives, and decision support.

Engagement of frontline staff, along with senior leadership, in competition-style healthcare-associated infection reduction efforts, combined with electronic clinical decision support tools, appeared to reduce antibiotic regimen initiations for urinary tract infections (P = .01). Mean monthly standardized infection and device utilization ratios also decreased (P < .003 and P < .0001, respectively).

The Rationale for a Mandatory Antibiotic Stewardship Rotation During Residency: What Worked, What Needs More Work.

Reports of antibiotic stewardship (AS) integration into the > 1000 United States internal medicine and family practice residency core curricula are scarce, but residents value such training. To help address this gap, and the projected shortage of physicians with training for establishing and leading an AS program (ASP), we describe the rationale for, and the output and shortcomings of, a dedicated AS rotation. Residents critically review, in real-time, inpatient antibiotic orders, provide feedback to the prescribers, learn the mechanics and requirements of an ASP, and complete a preliminary quality improvement project. Program evaluations are uniformly positive, noting limited opportunities otherwise to clarify optimal antibiotic choices or discuss antibiotics in depth. Nine posters at national conferences and 1 publication have roots in this rotation. Three alumni matriculated to accredited US infectious diseases fellowships. We invite others to join us in calling for more AS training opportunities during residency.

The Slow-Motion Catastrophe of Antimicrobial Resistance and Practical Interventions for All Prescribers.

All medical and surgical specialties depend on the pool of effective antibiotics that continues to evaporate because of the increasing prevalence of drug-resistant bacteria. Antimicrobial-resistant infections kill 700,000 patients every year. By 2050, they are projected to cause 10 million deaths per year at a cumulative global cost of $100 trillion. Professional societies and international health agencies, including the United Nations, have declared escalating antimicrobial resistance as one of the gravest and most urgent threats to global public health and issued calls for action. The propensity of bacteria to mobilize and share genetic resistance determinants across species and genera, record levels of conflict-driven human population displacement, and the dearth of new antibiotics and rapid diagnostic tests, along with climate change and the epidemic of opioid addiction, exacerbate the antimicrobial resistance crisis. The predominant cause of antibiotic resistance is exposure to antibiotics through appropriate and inappropriate use. Mindfulness, nudging by peers, and adjuncts and alternatives to antibiotics, such as phage therapies, microbiome-based therapies, and novel medical informatics applications, could help reduce antibiotic use. This article describes the antimicrobial resistance crisis and highlights points in the continuum of care in which clinicians can readily implement practical, no-cost changes to minimize antibiotic exposure.

Semi-Automated Visualization and ANalysis of Trends: A "SAVANT" for Facilitating Antimicrobial Stewardship Using Antistaphylococcal Resistance and Consumption as a Prototype.

BACKGROUND: Governments and health care regulators now require hospitals and nursing homes to establish programs to monitor and report antimicrobial consumption and resistance. However, additional resources were not provided. We sought to develop an approach for monitoring antimicrobial resistance and consumption that health care systems can implement with minimal added costs or modifications to existing diagnostic and informatics infrastructure. METHODS: Using (1) the electronic laboratory information system of a nationwide managed care network, (2) the 3 most widely used commercial microbiology diagnostic platforms, and (3) Staphylococcus aureus, one of the most common causes of infections worldwide, as a prototype, we validated the approach dubbed "SAVANT" for Semi-Automated Visualization and ANalysis of Trends. SAVANT leverages 3 analytical methods (time series analysis, the autoregressive integrated moving average, and generalized linear regression) on either commercial or open source software to report trends in antistaphylococcal use and resistance. RESULTS: All laboratory results from January 2010 through December 2015 from an annual average of 9.2 million health care beneficiaries were queried. Inpatient and outpatient prescription rates were calculated for 8 key antistaphylococcal compounds. Trends and relationships of antistaphylococcal consumption and resistance among 81 840 unique S. aureus isolates from >6.5 million cultures were revealed. CONCLUSIONS: Using existing or freely available resources, SAVANT was successfully implemented across a complex and geographically dispersed 280-hospital network, bridging a critical gap between medical informatics, large-scale data analytics, and mandatory reporting of health care quality metrics.

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells.

In light of the ongoing antimicrobial resistance crisis, there is a need to understand the role of co-pathogens, commensals, and the local microbiome in modulating virulence and antibiotic resistance. To identify possible interactions that influence the expression of virulence or survival mechanisms in both the multidrug-resistant organisms (MDROs) and human host cells, unique cohorts of clinical isolates were selected for whole genome sequencing with enhanced assembly and full annotation, pairwise co-culturing, and transcriptome profiling. The MDROs were co-cultured in pairwise combinations either with: (1) another MDRO, (2) skin commensals (Staphylococcus epidermidis and Corynebacterium jeikeium), (3) the common probiotic Lactobacillus reuteri, and (4) human fibroblasts. RNA-Seq analysis showed distinct regulation of virulence and antimicrobial resistance gene responses across different combinations of MDROs, commensals, and human cells. Co-culture assays demonstrated that microbial interactions can modulate gene responses of both the target and pathogen/commensal species, and that the responses are specific to the identity of the pathogen/commensal species. In summary, bacteria have mechanisms to distinguish between friends, foe and host cells. These results provide foundational data and insight into the possibility of manipulating the local microbiome when treating complicated polymicrobial wound, intra-abdominal, or respiratory infections.

Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital.

OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure. DESIGN Quasi-experimental observation. SETTING A 528-bed teaching hospital. PATIENTS The index case patient and 17 collocated ward mates. INTERVENTION Immediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology. RESULTS Candida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4-8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later. CONCLUSION Compared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations. Infect Control Hosp Epidemiol 2018;39:53-57.

Whole-Genome Analysis of Bartonella ancashensis, a Novel Pathogen Causing Verruga Peruana, Rural Ancash Region, Peru.

The genus Bartonella contains >40 species, and an increasing number of these Bartonella species are being implicated in human disease. One such pathogen is Bartonella ancashensis, which was isolated in blood samples from 2 patients living in Caraz, Peru, during a clinical trial of treatment for bartonellosis. Three B. ancashensis strains were analyzed by using whole-genome restriction mapping and high-throughput pyrosequencing. Genome-wide comparative analysis of Bartonella species showed that B. ancashensis has features seen in modern and ancient lineages of Bartonella species and is more related to B. bacilliformis. The divergence between B. ancashensis and B. bacilliformis is much greater than what is seen between known Bartonella genetic lineages. In addition, B. ancashensis contains type IV secretion system proteins, which are not present in B. bacilliformis. Whole-genome analysis indicates that B. ancashensis might represent a distinct Bartonella lineage phylogenetically related to B. bacilliformis.

Analysis of Serial Isolates of mcr-1-Positive Escherichia coli Reveals a Highly Active ISApl1 Transposon.

The emergence of a transferable colistin resistance gene (mcr-1) is of global concern. The insertion sequence ISApl1 is a key component in the mobilization of this gene, but its role remains poorly understood. Six Escherichia coli isolates were cultured from the same patient over the course of 1 month in Germany and the United States after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 as determined by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli isolates were collected during follow-up surveillance 9 months later. All isolates were analyzed by whole-genome sequencing (WGS). WGS revealed that the six initial isolates were composed of two distinct strains: an initial ST-617 E. coli strain harboring mcr-1 and a second, unrelated, mcr-1-negative ST-32 E. coli strain that emerged 2 weeks after hospitalization. Follow-up swabs taken 9 months later were negative for the ST-617 strain, but the mcr-1-negative ST-32 strain was still present. mcr-1 was associated with a single copy of ISApl1, located on a 64.5-kb IncI2 plasmid that shared >95% homology with other mcr-1 IncI2 plasmids. ISApl1 copy numbers ranged from 2 for the first isolate to 6 for the final isolate, but ISApl1 movement was independent of mcr-1 Some movement was accompanied by gene disruption, including the loss of genes encoding proteins involved in stress responses, arginine catabolism, and l-arabinose utilization. These data represent the first comprehensive analysis of ISApl1 movement in serial clinical isolates and reveal that, under certain conditions, ISApl1 is a highly active IS element whose movement may be detrimental to the host cell.

In Vivo Fitness Adaptations of Colistin-Resistant Acinetobacter baumannii Isolates to Oxidative Stress.

The loss of fitness in colistin-resistant (CR) Acinetobacter baumannii was investigated using longitudinal isolates from the same patient. Early CR isolates were outcompeted by late CR isolates for growth in broth and survival in the lungs of mice. Fitness loss was associated with an increased susceptibility to oxidative stress since early CR strains had reduced in vitro survival in the presence of hydrogen peroxide and decreased catalase activity compared to that of late CR and colistin-susceptible (CS) strains.

In vivo efficacy of humanized high dose meropenem and comparators against Pseudomonas aeruginosa isolates producing verona integron-encoded metallo-ß-lactamase (VIM).

INTRODUCTION: We aimed to describe the in vivo efficacy of meropenem, in addition to cefepime and levofloxacin as comparators against VIM-producing Pseudomonas aeruginosa and compare the findings to our previous observations with Enterobacteriaceae. METHODS: Eight clinical P. aeruginosa isolates with meropenem MICs from 4 to 512 mg/L were studied in a murine neutropenic thigh infection model. Animals were treated with doses of the antibiotics to simulate the human exposure of meropenem 2 g q8 h 30-min infusion, cefepime 2 g q8 h 30-min infusion and levofloxacin 500 mg q24 h. After 24 hours, the animals were euthanized and efficacy was calculated as the change in thigh bacterial density (log10 CFU) relative to the starting inoculum (0 h). RESULTS: As expected, levofloxacin was ineffective against all isolates due to their resistant phenotype (8 to>64 mg/L). Cefepime also showed minimal activity against all isolates consistent with its failure to achieve pharmacodynamic target exposures due to high MICs of 32 to>512 mg/L. In the presence of low MICs (4 to 16 mg/L), the fT> MIC of meropenem was sufficiently high to result in CFU reductions. However, conflicting activity was noted for isolates with MICs = 128 mg/L that possessed the same enzymatic profile, suggesting that other mechanisms of resistance are responsible for driving CFU outcomes. No activity was noted for organisms with a meropenem MIC = 512 mg/L. CONCLUSION: Unlike previous observations with MBL-producing Enterobacteriaceae that showed discordance between in vitro resistance and in vivo efficacy in the murine infection model, we found that the efficacy of humanized cefepime and meropenem was generally concordant with the phenotypic profile of VIM-producing P. aeruginosa.