The virome of the kitome: small circular virus-like genomes in laboratory reagents

In the course of studying the virome of protozoan parasites, we identified small circular genomes resembling viruses, which turned out to be contaminants from an RNA purification kit. We report their sequences here so others can detect possible contamination in their samples by aligning them to these targets.

The HIV-1 Capsid-Targeted Inhibitor GSK878 Alters Selection of Target Sites for HIV DNA Integration

Decades of effort have yielded highly effective antiviral agents to treat HIV, but viral strains have evolved resistance to each inhibitor type, focusing attention on the importance of developing new inhibitor classes. A particularly promising new target is the HIV capsid, the function of which can be disrupted by highly potent inhibitors that persist long term in treated subjects. Studies with such inhibitors have contributed to an evolving picture of the role of capsid itself-the inhibitors, like certain capsid protein (CA) amino acid substitutions, can disrupt intracellular trafficking to alter the selection of target sites for HIV DNA integration in cellular chromosomes. In this study, we compare effects on HIV integration targeting for two potent inhibitors-a new molecule targeting CA, GSK878, and the previously studied lenacapavir (LEN, formerly known as GS-6207). We find that both inhibitors reduce integration in active transcription units and near epigenetic marks associated with active transcription. A careful study of integration near repeated sequences indicated frequencies were also altered for integration within multiple repeat classes. One notable finding was increased integration in centromeric satellite repeats in the presence of LEN and GSK878, which is of interest because proviruses integrated in centromeric repeats have been associated with transcriptional repression, inducibility, and latency. These data add to the picture that CA protein remains associated with preintegration complexes through the point in infection during which target sites for integration are selected, and specify new aspects of the consequences of disrupting this mechanism.

MORBIDITY AND MORTALITY OF BINTURONGS (ARCTICTIS BINTURONG) IN UNITED STATES ZOOLOGICAL INSTITUTIONS (1986-2019)

Veterinary literature on diseases in binturong (Arctictis binturong) is often limited to case series or reports without population-level information. Morbidity and mortality data were collected from North American institutions through survey completion or submission of medical records. Responses included information about 74 individuals (37 males, 30 females, and 7 unknown neonates) representing 22 institutions, from 1986 to 2019. Antemortem data were available from 39 individuals, and postmortem data were available from 53 individuals. Eighteen individuals had both antemortem and postmortem records available. Age (mean ± SD) at death for adults (n = 41) was 15.2 ± 4.3 yr. Morbidity events were summarized by affected organ system; 160 events were reported. The systems with the most frequently reported events were gastrointestinal (33%; 53/160), integumentary (19%; 31/160), urinary (12%; 20/160), and musculoskeletal (19 [12%] of 160). Excluding neonates, primary causes of mortality included neoplasia (51%; 21/41), infectious or inflammatory diseases (24%; 10/41), and cardiovascular disease (17%; 7/41). Neoplasms (51%; 21/41) confirmed on histopathology included renal adenocarcinoma (47%; 10/21); mammary carcinoma (14%; 3/21); pancreatic islet cell carcinoma (2 [10%] of 21); and single instances of multicentric lymphoma, uterine carcinoma, and submucosal urethral adenoma. There were three additional cases of presumed neoplasia without histopathologic confirmation; masses were detected in the liver, heart base, and pancreas. Metastases were reported in 15 (71%) of 21 neoplasms. Although neoplasia and cardiovascular disease were common causes of mortality, they were rarely diagnosed antemortem. Neoplasia was often malignant and generally diagnosed after metastasis. Preventive medicine protocols with improved renal and cardiovascular evaluation are warranted and may result in earlier detection of subclinical disease in binturong.

Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States

Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.

The economic benefits of surgical site infection prevention in adults: a systematic review

BACKGROUND

Surgical site infections (SSIs) present a significant burden to healthcare and patients in terms of excess length of stay, distress, disability and death. SSI risk and the associated economic burden may be reduced through adherence to prevention guidelines although the irreducible minimum is unclear.

AIM

To evaluate the methods used to estimate the cost-effectiveness of prevention strategies for all SSIs.

METHODS

PubMed, Medline, CINAHL, and UK National Health Service Economic Evaluation Database were searched from inception to January 2020 to identify English language economic evaluation studies, embedded economic evaluations, and studies with some analysis in relation to cost and benefit in adult patients receiving surgical care in any setting. Risk of bias was assessed using two published checklists.

FINDINGS

Thirty-two studies involving 24,043 participants were included. Most studies evaluated SSI prevention in orthopaedic surgeries. Antibiotic prophylaxis, screening, treating, or decolonization of meticillin-resistant Staphylococcus aureus and surgical wound closure were the main methods evaluated. Methods ranged from cost-analyses to cost-effectiveness and cost-utility analyses. Synthesis of results was not possible due to heterogeneity. All studies reported some economic benefit associated with preventing SSI; however, measures of benefit were not reported consistently and the quality of studies was low to moderate. Limited evidence in relation to SSI impact on quality of life was identified.

CONCLUSION

Current evidence in relation to the economic benefits of SSI prevention is limited. Further robust studies that utilize sound economic and epidemiological methods are required to inform future investment decisions in SSI prevention.

Estimating excess length of stay due to healthcare-associated infections: a systematic review and meta-analysis of statistical methodology

BACKGROUND

Healthcare-associated infection (HCAI) affects millions of patients worldwide. HCAI is associated with increased healthcare costs, owing primarily to increased hospital length of stay (LOS) but calculating these costs is complicated due to time-dependent bias. Accurate estimation of excess LOS due to HCAI is essential to ensure that we invest in cost-effective infection prevention and control (IPC) measures.

AIM

To identify and review the main statistical methods that have been employed to estimate differential LOS between patients with, and without, HCAI; to highlight and discuss potential biases of all statistical approaches.

METHODS

A systematic review from 1997 to April 2017 was conducted in PubMed, CINAHL, ProQuest and EconLit databases. Studies were quality-assessed using an adapted Newcastle-Ottawa Scale (NOS). Methods were categorized as time-fixed or time-varying, with the former exhibiting time-dependent bias. Two examples of meta-analysis were used to illustrate how estimates of excess LOS differ between different studies.

FINDINGS

Ninety-two studies with estimates on excess LOS were identified. The majority of articles employed time-fixed methods (75%). Studies using time-varying methods are of higher quality according to NOS. Studies using time-fixed methods overestimate additional LOS attributable to HCAI. Undertaking meta-analysis is challenging due to a variety of study designs and reporting styles. Study differences are further magnified by heterogeneous populations, case definitions, causative organisms, and susceptibilities.

CONCLUSION

Methodologies have evolved over the last 20 years but there is still a significant body of evidence reliant upon time-fixed methods. Robust estimates are required to inform investment in cost-effective IPC interventions.

Assessment of manure phosphorus export through turfgrass sod production in Erath County, Texas

A best management practice (BMP) for exporting manure phosphorus (P) in turfgrass sod from the North Bosque River (NBR) watershed in central Texas was assessed using a geographic information system (GIS). The NBR watershed has a mandate to reduce the total annual P load to the NBR by 50% as a result of total maximum daily load regulation. Since dairy waste applications to fields are identified as the major nonpoint source of P to the river, innovative BMPs, such as export of manure P in turfgrass, will be needed to achieve the 50% reduction. However, methods are needed to evaluate the feasibility of these innovative management practices prior to their implementation. A geospatial database of suitable turfgrass production sites was developed for Erath County using GIS. Erath County largely encompasses the upper portion of the NBR watershed. Information from field experiments, production practices, and ground-truthing was used to search, analyze, and verify a geospatial database developed from national and regional sources. The integration and analyses of large databases supports the search by turf producers for sites suitable for turfgrass sod production in Erath County. In addition, GIS enables researchers and regulators to estimate manure P exports and reduced P loading due to implementation of the manure export BMP on a county scale. Under optimal conditions 198,000 kg manure P yr(-1) could be used and 114,840 kg manure P yr(-1) exported from the NBR watershed through implementation of a system using dairy manure to produce turfgrass sod. This is the equivalent of the manure P applied from 10,032 dairy cows yr(-1) and exported from 5808 dairy cows yr(-1). Application of GIS to large-scale planning and decision-making transcends traditional field-scale applications in precision agriculture.

Retinal pericytes control expression of nitric oxide synthase and endothelin-1 in microvascular endothelial cells

Pericytes are known to communicate with endothelial cells by direct contact and by releasing cytokines such as TGF-beta. There is also strong evidence that pericytes act as regulators of endothelial cell proliferation and differentiation. We have investigated the effect of pericyte-conditioned medium (PCM) on proliferation of human microvascular endothelial cells in vitro, together with the expression of the vasoregulatory molecules, constitutive and inducible nitric oxide synthases (ecNOS and iNOS), and endothelin-1 (ET-1). Expression was measured at the mRNA level using semiquantitative RT-PCR for all three genes and at the protein level for ecNOS and iNOS using Western blotting. Growth curves for HMECs showed that PCM inhibits proliferation, eventually leading to cell death. Exposure to PCM repressed iNOS mRNA expression fivefold after 6 h. A similar, though delayed, reduction in protein levels was observed. ecNOS mRNA was slightly induced at 6 h, though there was no significant change in ecNOS protein. By contrast, ET-1 mRNA was induced 2.3-fold after 6 h exposure to PCM. We conclude that pericytes release a soluble factor or factors that are potent inhibitors of endothelial cell growth and promote vasoconstriction by up-regulating endothelin-1 and down-regulating iNOS.

Isoelectric focusing and capillary zone electrophoretic studies using luteinizing hormone releasing hormone and its analog

Iontophoresis is the movement of charged compounds into and through the skin under an external electromotive force. A molecule's charge and size, as well as other factors, will determine its ability to be iontophoresed. One can gain insight into certain electrical aspects of a molecule by determining its isoelectric point as well as its electrophoretic mobility. In the present study, isoelectric focusing and capillary zone electrophoretic studies of luteinizing hormone releasing hormone, (LHRH) and one of its analogs are performed in order to predict their ability to be iontophoresed. The pI of LHRH is determined to be 9.6 while that of its free acid is 6.9. In addition, it is concluded that although the two compounds are chemically similar, the native compound is more mobile at pH > 2.5. These results suggest that the native compound might be better suited for iontophoretic delivery than is the free-acid analog.

Prophylactic doxycycline for travelers' diarrhea in Thailand. Further supportive evidence of Aeromonas hydrophila as an enteric pathogen

A randomized double-blind study to determine the efficacy of a three-week course of doxycycline (100 mg daily) in preventing travelers' diarrhea was performed in 1980 among 63 United States Peace Corps volunteers during their first five weeks in Thailand, an area where doxycycline-resistant enterotoxigenic Escherichia coli are known to be common. Eight (24%) of 33 volunteers taking placebo and 3 (10%) of 30 taking doxycycline developed travelers' diarrhea for a calculated protection of 59%, but this was not statistically significant (p = 0.12). Aeromonas hydrophila was isolated from 8 to 19 volunteers with either travelers' diarrhea or mild diarrhea in the placebo group, but from only 1 of 12 in the doxycycline group (p less than or equal to 0.05). Furthermore, doxycycline significantly prevented colonization of the gastrointestinal tract with A. hydrophila while it was being taken (p less than or equal to 0.01). Enterotoxigenic E. coli was isolated from only one volunteer with travelers' diarrhea in the placebo group and from none in the doxycycline group. Doxycycline prophylaxis of travelers' diarrhea in this geographic area, though not shown to be significantly protective, further supports the role of A. hydrophila as an enteric pathogen.

Prevalence of heat-stable II enterotoxigenic Escherichia coli in pigs, water, and people at farms in Thailand as determined by DNA hybridization

The DNA hybridization assay employing a 460-base-pair fragment of DNA encoding for the methanol-insoluble form of heat-stable toxin (ST-II) was used to determine the prevalence of ST-II enterotoxigenic Escherichia coli (ETEC) in pigs, people, and water at 57 farms in Sri Racha, Thailand. ST-II ETEC was found in 62 (3%) of 2,110 suckling, 181 (32%) of 560 weaned, and 4 (1%) of 457 adult pigs examined. Of 62 suckling pigs with ST-II ETEC infections 21% had diarrhea, but none of 185 infected older pigs had diarrhea. ST-II ETEC was found more frequently in suckling pigs with diarrhea than without diarrhea (13 of 146 versus 49 of 1,964) (P less than 0.001). ST-II ETEC was detected in water collected from 3 of 57 clay jars containing water used to bathe at three pig farms, in 1 jar used to bathe immediately after working in the barn, and from one farmer who did not have a recent history of diarrhea. Evidence of this organism was not found in 245 other individuals living on the pig farms or in 220 inhabitants and 114 water specimens collected at tapioca farms nearby. In Thailand ST-II ETEC was found in suckling pigs with diarrhea but was infrequently found in humans.

Flies as a source of enteric pathogens in a rural village in Thailand

The village of Ban Pong in northeastern Thailand was studied from January through December 1981 to determine the importance of flies as a source of enteric pathogens. The number of flies (predominantly Musca domestica) increased in kitchens and animal pens in the hot dry spring, when the incidence of diarrhea was highest in the village. Enterotoxigenic Escherichia coli, Shigella spp., non-O1 Vibrio cholerae, and Vibrio fluvalis were isolated from fly pools in yards (69%), animal pens (38%), bathrooms (35%), and kitchens (8%). Enterotoxigenic E. coli was isolated from one fly pool in May and from another in June, when the incidence of such infections was highest in the village. Flies often carry and presumably disseminate enteric pathogens in rural Thailand.

Diagnosis of gonorrhoea using a genetic transformation test at a venereal disease clinic in Thailand

A genetic transformation test (GTT), a technique in which gonococcal DNA is detected in clinical specimens, was used to search for Neisseria gonorrhoeae infections in 37 men and 159 women at the Venereal Disease clinic in Cholburi, Thailand. Swabs were collected in duplicate from cervical specimens from 159 women and from urethral specimens from 37 men. One of each specimen was cultured on Thayer-Martin media while the other was mailed to the United States at room temperature for the GTT which involved a delay of 10 to 14 days. With the urethral specimens N. gonorrhoeae was identified in 84% (31/37) of specimens and there was 100% concordance between the results of the GTT and culturing specimens directly on Thayer-Martin media. With cervical specimens N. gonorrhoeae was isolated from 26% (41/159) by the standard culture technique and 19% (13/159) by the GTT. Seventy-six percent of the culture positive specimens were positive with the GTT and two specimens from which N. gonorrhoeae were not isolated were positive in the GTT. The GTT technique enables physicians to send swab collected from patient with suspected gonorrhoea without any special transport media to a central laboratory for laboratory diagnosis of gonorrhoeal infections. This technique which uses reagents which are available in most bacteriology laboratories, should facilitate surveillance of gonorrhoea especially when specimens are collected in clinics where bacteriology laboratory facilities are not available.