Comparative genomic analysis of four multidrug-resistant isolates of Acinetobacter baumannii from Georgia.

OBJECTIVES: This study reports the draft genomes of four newly isolated multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) isolates (0830, 0365, 4022, and 2846) from western Georgia to identify putative antimicrobial resistance genes (ARGs) and to determine the clonal subtypes of local clinical isolates. METHODS: An Illumina MiSeq sequencer was used to perform whole-genome sequencing (WGS). The Vitek 2 automated system was used for microbial identification and antimicrobial resistance profiling. RESULTS: Taxonomical identification as A. baumannii was confirmed by WGS. In silico analyses resolved their ARG content and clonal relatedness using the Oxford (Oxf) and Pasteur (Pas) multi-locus sequence typing schemes. Isolates 0365 and 4022 displayed similar allelic profiles corresponding to ST944Oxf/ST78Pas. Isolate 2846 displayed a different allelic profile consistent with ST19Pas/IC 1 (International or European Clone I) and exhibited a novel Oxford ST that was designated as 1868. Isolate 0830 displayed the ST78Pas allelic profile, similar to isolates 0365 and 4022, and also possessed a single allelic mismatch in the gpi gene, resulting in an ST1104Oxf allele profile in the Oxford typing scheme. CONCLUSION: Circulating MDR A. baumannii exhibited genetic heterogeneity with variations in the structure and content of genomic A. baumannii resistance islands and encoded multiple putative ARGs. This report represents the first clonal subtype information and genomic characterization of MDR A. baumannii in Georgia and may inform future epidemiological investigations.

Melioidosis after Hurricanes Irma and Maria, St. Thomas/St. John District, US Virgin Islands, October 2017.

We report 2 cases of melioidosis in women with diabetes admitted to an emergency department in the US Virgin Islands during October 2017. These cases emerged after Hurricanes Irma and Maria and did not have a definitively identified source. Poor outcomes were observed when septicemia and pulmonary involvement were present.

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.

Chromosomally Encoded mcr-5 in Colistin-Nonsusceptible Pseudomonas aeruginosa.

Whole-genome sequencing (WGS) of historical Pseudomonas aeruginosa clinical isolates identified a chromosomal copy of mcr-5 within a Tn3-like transposon in P. aeruginosa MRSN 12280. The isolate was nonsusceptible to colistin by broth microdilution, and genome analysis revealed no mutations known to confer colistin resistance. To the best of our knowledge, this is the first report of mcr in colistin-nonsusceptible P. aeruginosa.

Bacteraemia due to Microbacterium paraoxydans in a patient with chronic kidney disease, refractory hypertension and sarcoidosis.

INTRODUCTION: Microbacterium spp. are yellow-pigmented Gram-positive coryneform rods found in various environmental sources, such as soil and water samples. They rarely cause human infection, mostly infecting immunocompromised patients and catheter insertion sites, making them challenging to identify in clinical settings. CASE PRESENTATION: We report a case of a 61-year-old female on long-term prednisone therapy for sarcoidosis with minimal exposure to environmental sources, who presented with an overtly infected Hickman catheter site and presyncope. The patient had a central venous catheter (CVC) that had been in place for the previous 6 years for treatment of refractory hypertension and congestive heart failure. Blood cultures obtained from the CVC on initial presentation were positive for a mixed infection, which was subcultured and grew Staphylococcus aureus, Staphylococcus epidermidis, Acinetobacter radioresistens and Leifsonia aquatica based on the Becton Dickinson Phoenix Automated Microbiology System. The L. aquatica, designated as isolate 4120, was further analysed, since infections associated with this organism are uncommon, and it was the only organism to grow from the patient's catheter tip. Matrix-assisted laser desorption ionization-time of flight MS identified isolate 4120 as Microbacterium paraoxydans. To resolve the conflicting results, additional analyses of isolate 4120 were carried out and compared to several reference strains. Isolate 4120 was found to have intermediate susceptibility to ciprofloxacin and non-susceptibility to vancomycin. Morphology, susceptibility, biochemical characteristics and whole-genome sequencing confirmed the clinical isolate as Microbacterium paraoxydans. CONCLUSION: In this case, we identified an organism that is rarely seen in clinical settings and characterized it with a comprehensive laboratory analysis. The patient in our case responded to replacement of the CVC, and treatment with levofloxacin by mouth and intravenous vancomycin.

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.

Adherence to published antimicrobial prophylaxis guidelines for wounded service members in the ongoing conflicts in Southwest Asia.

In 2008, a clinical practice guideline (CPG) was developed for the prevention of infections among military personnel with combat-related injuries. Our analysis expands on a prior 6-month evaluation and assesses CPG adherence with respect to antimicrobial prophylaxis for U.S. combat casualties medically evacuated to Landstuhl Regional Medical Center over a 1-year period (June 2009 through May 2010), with an eventual goal of continuously monitoring CPG adherence and measuring outcomes as a function of compliance. We classified adherence to the CPG as receipt of recommended antimicrobials within 48 hours of injury. A total of 1106 military personnel eligible for CPG assessment were identified and 74% received antimicrobial prophylaxis. Overall, CPG compliance within 48 hours of injury was 75%. Lack of antimicrobial prophylaxis contributed 2 to 22% to noncompliance varying by injury category, whereas receipt of antibiotics other than preferred was 11 to 30%. For extremity injuries, antimicrobial prophylaxis adherence was 60 to 83%, whereas it was 80% for closed injuries and 68% for penetrating abdominal injuries. Overall, the results of our analysis suggest an ongoing need to improve adherence, monitor CPG compliance, and assess effectiveness.

In vitro and in vivo activity of first generation cephalosporins against Leptospira.

Third generation cephalosporins are commonly used in the treatment of leptospirosis. The efficacy of first generation cephalosporins has been less well-studied. Susceptibility testing of 13 Leptospira strains (11 serovars) to cefazolin and cephalexin was conducted using broth microdilution. Median minimal inhibitory concentration (MIC) for cefazolin and cephalexin ranged from < 0.016 to 2 µg/mL (MIC(90) = 0.5 µg/mL) and from 1 to 8 µg/mL (MIC(90) = 8 µg/mL), respectively. Efficacy of cefazolin and cephalexin in an acute lethal hamster model of leptospirosis was studied. Survival rates for cefazolin were 80%, 100%, and 100%, and survival rates for cephalexin were 50%, 80%, and 100% (treated with 5, 25, and 50 mg/kg per day for 5 days, respectively). Each treatment group showed improved survival compared with no treatment (P < 0.01), and none of the therapies, regardless of dose, was statistically significantly different than doxycycline. These results support a potential role for first generation cephalosporins as alternative therapies for leptospirosis.

Efficacy of minocycline and tigecycline in a hamster model of leptospirosis.

Leptospirosis is a widespread zoonotic infection characterized by acute febrile illness. Severely ill patients may require empiric treatment with broad-spectrum antibiotics prior to definitive diagnosis. We evaluated the efficacy of minocycline and tigecycline against leptospirosis in a hamster model. Hamsters were treated with either minocycline (5, 10, or 25 mg/kg per day) or tigecycline (5, 10, or 25 mg/kg per day) for 5 days. Controls included untreated animals and doxycycline-treated animals (5 mg/kg per day). Nine days after infection, all untreated animals were dead. All treated hamsters survived to the end of study (day 21). Study groups showed significantly improved survival compared to the untreated group (P < .01). Minocycline and tigecycline showed survival benefit comparable to the standard treatment, doxycycline. In the absence of doxycycline, minocycline may be considered as an alternative, while tigecycline may be useful in the management of severely ill patients prior to a definitive diagnosis.

History of infections associated with combat-related injuries.

Despite the innumerable variations in war-making throughout the millennia, wounds have always been characterized by devitalized tissue, the presence of foreign bodies, clots, fluid collection, and contamination by microorganisms. Even in the postantibiotic era, infections of these wounds remain a significant contributor to both morbidity and mortality. Shifts in causal organisms and their resistance profiles continue to challenge each new generation of therapeutics. This article reviews the history of war wound infections, with an emphasis on wound microbiology and combat casualty management during US conflicts from World War I through the end of 20th century.