Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by its chronological detection across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range. 870 high-quality nuclear single nucleotide polymorphic DNA markers identified five distinct New World population clusters, broadly reflecting FAW native geographical ranges and the absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinning the pest’s global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated the potential of population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

SUMMARY Vancomycin-resistant Enterococcus bloodstream infections (VRE-BSI) are a growing problem with few clinical trials to guide therapy. We conducted a retrospective study of management and predictors of mortality for VRE-BSI at a tertiary care centre from January 2005 to August 2008. Univariate and multivariable analyses examined the relationship of patient characteristics and antibiotic therapy with 30-day all-cause mortality. Rates of VRE-BSI increased from 0.06 to 0.17 infections/thousand patient days (p=0.03). Among 235 patients, 30-day mortality was 34.9%. Patients were primarily treated with linezolid (44.2%) or daptomycin (36.5%). Factors associated with mortality were haemodialysis (OR 3.2, 95% CI 1.6-6.3, p=0.007), mechanical ventilation (OR 3.7, 95% CI 1.3-10.4, p=0.01), and malnutrition (OR 2.0, 95% CI 1.0-4.0, p=0.046). Use of linezolid, but not daptomycin (p=0.052) showed a trend toward an association with survival. In conclusion, VRE-BSI is a growing problem, associated with significant 30-day mortality. Multiple factors were associated with poor outcomes at our hospital.

Identification ofBemisia tabacicryptic whitefly species complex currently relies on molecular characterisation of the mitochondrial DNA cytochrome oxidase subunit I (mtCOI) partial gene, however, nuclear mitochondrial sequences (NUMTs), PCR-derived pseudogenes and/or poor sequence editing have hindered this effort. To-date,ca.5,175 partial (≥ 300bp) mtCOI sequences for species identification purposes have been reported. We reviewedca.10% of sequences representing the standardB. tabacispecies complex mtCOI dataset. We found that 333 sequences (64.9%) were NUMTs, pseudogenes and/or affected by poor sequence quality. Amino acid pattern analyses of high throughput sequencing-derived mtCOI gene from 24 ‘tabaci’ and ‘non-tabaci’ species enabled differentiation between NUMTs/pseudogene-affected and likely real mtCOI sequences, and that the SSA4, SSA5/SSA8, AsiaII-2 and AsiaII_4 species were NUMTs/pseudogenes artefacts. Intra-specific uncorrected nucleotide distances (p-dist) from our up-dated dataset ranged from 0-1.98%, inter-specificp-dist within phylogenetic clades ranged betweenca.2.5 and 8%, and 8 and >19% for species between phylogenetic clades. Differentiating between closely related species could therefore utilise an ‘average’p-dist of 2.5%. Despite the smallerB. tabacimtCOI dataset, six putative new species were identified. Adoption of our standardised workflow and up-dated mtCOI clean dataset could facilitate better diagnostics ofB. tabaciand ‘non-tabaci’ cryptic species.

Background Pneumocystis jiroveci pneumonia is a life-threatening infection for immunocompromised individuals. There are robust data and clear guidelines for prophylaxis and treatment of HIV-related Pneumocystis jiroveci pneumonia (HIV-PCP), yet few data and no guidelines for non-HIV related Pneumocystis pneumonia (NH-PCP). We postulated that prevention and inpatient management of HIV-PCP differed from NH-PCP. Methods We performed a retrospective case review of all pathologically confirmed cases of PCP seen at the University of Alabama Medical Center from 1996 to 2008. Data on clinical presentation, hospital course, and outcome were collected using a standardized data collection instrument. Bivariate analysis compared prophylaxis, adjunctive corticosteroids, and clinical outcomes between patients with HIV-PCP and NH-PCP. Results Our analysis of the cohort included 97 cases of PCP; 65 HIV and 32 non-HIV cases. Non-HIV cases rarely received primary prophylaxis (4% vs. 38%, p=0.01) and received appropriate antibiotics later in the course of hospitalization (5.2 vs 1.1 days, P<0.005). Among transplant patients, NH-PCP was diagnosed a mean of 1,066 days after transplantation and most patients were on low-dose corticosteroids (87%) at the time of disease onset. No significant differences in adjunctive corticosteroid use (69% vs. 77%, p=0.39) and 90-day mortality (41% vs. 28%, p=0.20) were detected. Conclusions Patients who have undergone organ or stem cell transplant remain at risk for PCP for many years after transplantation. In our cohort, patients who developed NH-PCP were rarely given prophylaxis and initiation of appropriate antibiotics was significantly delayed compared to cases of HIV-PCP. Medical providers should be aware of the ongoing risk for NH-PCP, even late after transplantation, and consider more aggressive approaches to both prophylaxis and earlier empiric therapy for PCP.

Objective Vancomycin-resistant Enterococci (VRE) have become a public health concern with implications for patient mortality and costs. Hospital antibiotic usage may impact VRE incidence, but the relationship is poorly understood. Animal investigations suggest ceftriaxone may be associated with VRE proliferation. We measured antimicrobial usage and VRE bloodstream infection (BSI) incidence to test our hypothesis that increased ceftriaxone use would be associated with a higher incidence of VRE-BSI. Setting The University of Alabama at Birmingham Medical Center is a 900-bed urban tertiary-care hospital Methods Retrospective analysis of antimicrobial usage and VRE-BSI from 2005 to 2008 (43 months). Antimicrobial usage quantified as days of therapy/1,000 patient-days (DOT). VRE-BSI incidence calculated as cases/1,000 patient-days. Negative binomial regression with adjustment for correlation between consecutive observations measured the association between antimicrobial usage and VRE-BSI incidence at the hospital- and care-unit levels. Results VRE-BSI incidence increased from 0.06 to 0.17 infections/1,000 patient-days. Hospital VRE-BSI incidence was associated with prior-month ceftriaxone DOT (Incidence Rate Ratio 1.38 per 10 DOT; p=0.005). After controlling for ceftriaxone, prior-month cephalosporin use (class) was not predictive of VRE-BSI (p=0.70). Similarly, prior-month use of piperacillin-tazobactam, ceftazidime, cefepime, cefazolin, or vancomycin was not predictive of VRE-BSI when considered individually (p≥0.4 for all comparisons). The final model suggests that type of intensive care unit was related to VRE-BSI incidence. Conclusions Ceftriaxone use in the prior month, but not cephalosporin (class) or vancomycin use, was related to VRE-BSI incidence. These findings suggest that an antimicrobial stewardship program that limits ceftriaxone may reduce nosocomial VRE-BSI incidence.