An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species.

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study.

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

Observed electric charge of insect swarms and their contribution to atmospheric electricity.

The atmosphere hosts multiple sources of electric charge that influence critical processes such as the aggregation of droplets and the removal of dust and aerosols. This is evident in the variability of the atmospheric electric field. Whereas these electric fields are known to respond to physical and geological processes, the effect of biotic sources of charge has not hitherto been considered. Here, we combine theoretical and empirical evidence to demonstrate that honeybee swarms directly contribute to atmospheric electricity, in proportion to the swarm density. We provide a quantitative assessment of this finding, by comparing the electrical contribution of various swarming insect species with common abiotic sources of charge. This reveals that the charge contribution of some insect swarms will be comparable with that of meteorologically induced variations. The observed transport of charge by insects therefore demonstrates an unexplored role of biogenic space charge for physical and ecological processes in the atmosphere.

Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human Illness

Extraintestinal pathogenic Escherichia coli (ExPEC) cause urinary tract and potentially life-threatening invasive infections. Unfortunately, the origins of ExPEC are not always clear. We used genomic data of E. coli isolates from five U.S. government organizations to evaluate potential sources of ExPEC infections. Virulence gene analysis of 38,032 isolates from human, food animal, retail meat, and companion animals classified the subset of 8142 non-diarrheagenic isolates into 40 virulence groups. Groups were identified as low, medium, and high relative risk of containing ExPEC strains, based on the proportion of isolates recovered from humans. Medium and high relative risk groups showed a greater representation of sequence types associated with human disease, including ST-131. Over 90% of food source isolates belonged to low relative risk groups, while >60% of companion animal isolates belonged to medium or high relative risk groups. Additionally, 18 of the 26 most prevalent antimicrobial resistance determinants were more common in high relative risk groups. The associations between antimicrobial resistance and virulence potentially limit treatment options for human ExPEC infections. This study demonstrates the power of large-scale genomics to assess potential sources of ExPEC strains and highlights the importance of a One Health approach to identify and manage these human pathogens.

Surveillance of antimicrobial resistance in veterinary medicine in the United States: Current efforts, challenges, and opportunities.

Antimicrobial resistance (AMR) is a global problem facing human, animal, plant, and environmental health by threatening our ability to effectively treat bacterial infections with antimicrobials. In the United States, robust surveillance efforts exist to collect, analyze, and disseminate AMR data in human health care settings. These tools enable the development of effective infection control methods, the detection of trends, and provide the evidence needed to guide stewardship efforts to reduce the potential for emergence and further spread of AMR. However, in veterinary medicine, there are currently no known equivalent tools. This paper reviews efforts in the United States related to surveillance of AMR in veterinary medicine and discusses the challenges and opportunities of using data from veterinary diagnostic laboratories to build a comprehensive AMR surveillance program that will support stewardship efforts and help control AMR in both humans and animals.

Genome Sequences of Mycobacterium Strains Recovered from Captive Elephants with Tuberculosis.

Members of the Mycobacterium tuberculosis complex cause tuberculosis, infamous for enormous impacts on human health. As zoonoses, they also threaten endangered species like African/Asian elephants. We report the whole-genome sequences of Mycobacterium tuberculosis bv. tuberculosis and Mycobacterium tuberculosis bv. bovis from two zoo elephants in the United States.

Next-generation sequencing capacity and capabilities within the National Animal Health Laboratory Network.

With the cost of next-generation sequencing (NGS) decreasing, this technology is rapidly being integrated into the workflows of veterinary clinical and diagnostic laboratories nationwide. The mission of the U.S. Department of Agriculture-National Animal Health Laboratory Network (NAHLN) is in part to evaluate new technologies and develop standardized processes for deploying these technologies to network laboratories for improving detection and response to emerging and foreign animal diseases. Thus, in 2018, the NAHLN identified the integration of NGS into the network as a top priority. In order to assess the current state of preparedness across NAHLN laboratories and to identify which have the capability for performing NGS, a questionnaire was developed by the NAHLN Methods Technical Working Group and submitted to all NAHLN laboratories in December 2018. Thirty of 59 laboratories completed the questionnaire, of which 18 (60%) reported having some sequencing capability. Multiple sequencing platforms and reagents were identified, and limited standardized quality control parameters were reported. Our results confirm that NGS capacity is available within the NAHLN, but several gaps remain. Gaps include not having sufficient personnel trained in bioinformatics and data interpretation, lack of standardized methods and equipment, and maintenance of sufficient computing capacity to meet the growing demand for this technology.

A survey of methods used for antimicrobial susceptibility testing in veterinary diagnostic laboratories in the United States.

Antimicrobial resistance is a serious threat to animal and human health worldwide, requiring a collaborative, holistic approach. The U.S. Government has developed a national strategy to address antimicrobial resistance, with one component being to monitor antimicrobial resistance in agricultural settings. We developed a survey to collect information about antimicrobial susceptibility testing (AST) from the veterinary diagnostic laboratory community in the United States, assessing current practices and technologies and determining how AST information is shared. Of the 132 surveys administered, 52 (39%) were returned. Overall, responding laboratories conducted susceptibility tests on 98,788 bacterial isolates in 2014, with Escherichia coli being the most common pathogen tested across all animal species. The 2 most common AST methods employed were the disk diffusion method (71%) and the Sensititre platform broth microdilution system (59%). Laboratories primarily used the Clinical Laboratory Standards Institute (CLSI) VET-01 standard (69%) and the automatically calculated interpretations provided by the commercial AST systems (61%) for interpreting their AST data. Only 22% of laboratories published AST data on a periodic basis, usually via annual reports published on the laboratory's website or through peer-reviewed journals for specific pathogens. Our results confirm that disk diffusion and broth microdilution remain the standard AST methods employed by U.S. veterinary diagnostic laboratories, and that CLSI standards are commonly used for interpreting AST results. This information will help determine the most efficient standardized methodology for future surveillance. Furthermore, the current infrastructure within laboratories, once harmonized, will help provide a mechanism for conducting national surveillance programs.

Brucellosis Transmission between Wildlife and Livestock in the Greater Yellowstone Ecosystem: Inferences from DNA Genotyping.

The wildlife of the Greater Yellowstone Ecosystem carries brucellosis, which was first introduced to the area by cattle in the 19th century. Brucellosis transmission between wildlife and livestock has been difficult to study due to challenges in culturing the causative agent, Brucella abortus . We examined B. abortus transmission between American bison ( Bison bison ), Rocky Mountain elk ( Cervus elaphus nelsoni), and cattle ( Bos taurus ) using variable number tandem repeat (VNTR) markers on DNA from 98 B. abortus isolates recovered from populations in Idaho, Montana, and Wyoming, US. Our analyses reveal interspecies transmission. Two outbreaks (2007, 2008) in Montana cattle had B. abortus genotypes similar to isolates from both bison and elk. Nevertheless, similarity in elk and cattle isolates from the 2008 outbreak suggest that elk are the likely source of brucellosis transmission to cattle in Montana and Wyoming. Brucella abortus isolates from sampling in Montana appear to be divided in two clusters: one found in local Montana elk, cattle, and bison; and another found mainly in elk and a bison from Wyoming, which is consistent with brucellosis having entered Montana via migration of infected elk from Wyoming. Our findings illustrate complex patterns of brucellosis transmission among elk, bison, and cattle as well as the utility of VNTRs to infer the wildlife species of origin for disease outbreaks in livestock.

Milieu improvement in psychiatry using evidence-based practices: the long and winding road of culture change.

BACKGROUND: Shorter inpatient stays have resulted in greater patient acuity, making it difficult for patients to heal and challenging for staff to manage. OBJECTIVE: To improve the milieu for psychiatric inpatients using evidence-based practices. DESIGN: A thorough literature review suggested 18 basic principles to improve patient outcomes while reducing violence, seclusion, restraint, and 1:1 observation. Interventions were multiple, including intensive multi-modal staff education based on the literature review and starting in orientation, introduction of comfort rooms, changes in debriefing practices, careful review of all seclusion and restraint episodes, introduction of integrative modalities, and careful review of all 1:1 observation and review of unit structure. RESULTS: Multiple interventions resulted in favorable outcomes in the following: rates of seclusion and restraints; time devoted to 1:1 observation, patient and staff satisfaction; violent incidents; and staff and patient injury. CONCLUSIONS: Long-term culture change toward a more therapeutic milieu can occur as a result implementing evidence-based practices.

The green operating room: simple changes to reduce cost and our carbon footprint.

Generating over four billion pounds of waste each year, the healthcare system in the United States is the second largest contributor of trash with one-third produced by operating rooms. Our objective is to assess improvement in waste reduction and recycling after implementation of a Green Operating Room Committee (GORC) at our institution. A surgeon and nurse-initiated GORC was formed with members from corporate leadership, nursing, anesthesia, and OR staff. Initiatives for recycling opportunities, reduction of energy and water use as well as solid waste were implemented and the results were recorded. Since formation of GORC in 2008, our OR has diverted 6.5 tons of medical waste. An effort to recycle all single-use devices was implemented with annual solid waste reduction of approximately 12,860 lbs. Disposable OR foam padding was replaced with reusable gel pads at greater than $50,000 per year savings. Over 500 lbs of previously discarded batteries were salvaged from the OR and donated to charity or redistributed in the hospital ($9,000 annual savings). A "Power Down" initiative to turn off all anesthesia and OR lights and equipment not in use resulted in saving $33,000 and 234.3 metric tons of CO2 emissions reduced per year. Converting from soap to alcohol-based waterless scrub demonstrated a potential saving of 2.7 million liters of water annually. Formation of an OR committee dedicated to ecological initiatives can provide a significant opportunity to improve health care's impact on the environment and save money.

Isolation of mycobacteria from clinical samples collected in the United States from 2004 to 2011.

BACKGROUND: Mycobacteria other than M. bovis may interfere with current bovine tuberculosis diagnostic tests resulting in false positive test results. As the prevalence of M. bovis decreases in the United States, interference from other mycobacteria play an increasingly important role in preventing the eradication of M. bovis. To identify mycobacteria other than M. bovis that may be interfering with current diagnostic tests, a retrospective study was performed to identify mycobacteria isolated from clinical tissues at the National Veterinary Services Laboratories between 1 January 2004 and 9 October 2011. RESULTS: During the study period, 2,366 mycobacteria other than M. bovis were isolated from samples submitted for clinical diagnosis of M. bovis. Fifty-five mycobacterial species were isolated during this time period. In cattle, M. avium complex, M. fortuitum/fortuitum complex, M. smegmatis, M. kansasii, and M. terrae complex were the predominate species other than M. bovis isolated from tissues submitted for culture. Mycobacteria other than M. bovis isolated from deer were predominantly M. avium complex, M. terrae/terrae complex, and M. fortuitum/fortuitum complex. CONCLUSIONS: These data provide information characterizing the species and relative prevalence of mycobacteria other than M. bovis that may interfere with current diagnostic tests.

Comparison of the MGIT 960, BACTEC 460 TB and solid media for isolation of Mycobacterium bovis in United States veterinary specimens.

BACKGROUND: Bacteriologic culture remains one of the most important methods to diagnose bovine tuberculosis despite the lengthy incubation time, significant decontamination and media expense, and high biocontainment requirements. Media selection is an important determination of culture sensitivity, and the planned discontinuation of the BACTEC 460 TB culture system has challenged veterinary diagnostic laboratories to evaluate alternatives. At the National Veterinary Services Laboratories the BACTEC MGIT 960 and 4 solid media formulations were compared with the BACTEC 460 TB system on 6,795 veterinary diagnostic specimens submitted for Mycobacterium bovis culture. RESULTS: M. bovis was isolated from 2.6% of the samples and atypical mycobacteria from 4.4% of the samples. The BACTEC 12B media isolated significantly more M. bovis (93.1% of positive samples) than MGIT 960 media (81.9%). However, contamination rates were much higher for the MGIT media, 17-24%, compared to 7% for BACTEC, suggesting that contamination was a major cause of MGIT reduced sensitivity. Time to signal positive was 2.37 weeks (95% CI 2.24-2.5) for the MGIT, and 3.2 weeks (95% CI 3.07-3.3) for the BACTEC, both earlier than any solid media. Mycobactosel LJ failed to isolate M. bovis from primary culture. An in-house 7H11 media supplemented with calf sera, hemolyzed blood, malachite green and pyruvate recovered more M. bovis (80.6%) with the least amount of contamination of any other solid media evaluated. CONCLUSION: Decontamination methods may have to be optimized and or MGIT media may have to be altered to reduce contamination in veterinary samples. Despite these issues, the MGIT 960 system is still favored over the use of solid media due to decreased time to recovery and the potential for higher sensitivity.

Molecular epidemiology of Brucella abortus isolates from cattle, elk, and bison in the United States, 1998 to 2011.

A variable-number tandem repeat (VNTR) protocol targeting 10 loci in the Brucella abortus genome was used to assess genetic diversity among 366 field isolates recovered from cattle, bison, and elk in the Greater Yellowstone Area (GYA) and Texas during 1998 to 2011. Minimum spanning tree (MST) and unweighted-pair group method with arithmetic mean (UPGMA) analyses of VNTR data identified 237 different VNTR types, among which 14 prominent clusters of isolates could be identified. Cattle isolates from Texas segregated into three clusters: one comprised of field isolates from 1998 to 2005, one comprised of vaccination-associated infections, and one associated with an outbreak in Starr County in January 2011. An isolate obtained from a feral sow trapped on property adjacent to the Starr County herd in May 2011 clustered with the cattle isolates, suggesting a role for feral swine as B. abortus reservoirs in Starr County. Isolates from a 2005 cattle outbreak in Wyoming displayed VNTR-10 profiles matching those of strains recovered from Wyoming and Idaho elk. Additionally, isolates associated with cattle outbreaks in Idaho in 2002, Montana in 2008 and 2011, and Wyoming in 2010 primarily clustered with isolates recovered from GYA elk. This study indicates that elk play a predominant role in the transmission of B. abortus to cattle located in the GYA.

Improved specificity for detection of Mycobacterium bovis in fresh tissues using IS6110 real-time PCR.

BACKGROUND: Culture of M. bovis from diagnostic specimens is the gold standard for bovine tuberculosis diagnostics in the USA. Detection of M. bovis by PCR in tissue homogenates may provide a simple rapid method to complement bacterial culture. A significant impediment to PCR based assays on tissue homogenates is specificity since mycobacteria other than M. bovis may be associated with the tissues. RESULTS: Previously published IS6110 based PCR diagnostic assays, along with one developed in house, were tested against environmental mycobacteria commonly isolated from diagnostic tissues submitted to the National Veterinary Services Laboratory. A real-time PCR assay was developed (IS6110_T) that had increased specificity over other IS6110 based assays. Of the 13 non-tuberculous mycobacteria tested with IS6110_T only M. wolinskyi was positive. Thirty M. bovis infected tissue homogenates and 18 control tissues were used to evaluate the potential for the assay as a diagnostic test. In this small sample, IS6110_T detected 20/30 samples from M. bovis infected animals and 0/18 control tissues. CONCLUSIONS: The IS6110_T assay provides a PCR based assay system that is compatible with current diagnostic protocols for the detection of M. bovis in the USA and compliments current testing strategies.

Improving care on mental health wards with hourly nurse rounds.

Hourly rounds are becoming more popular on inpatient medical wards and are known to be beneficial to patients and nurses. However, there is little evidence about their impact in psychiatry and what hourly rounds would look like on inpatient mental health units. This article examines the introduction of hourly nurse rounds on inpatient mental health wards in an American hospital, and how they were adapted to the needs of psychiatric patients. The positive effects on patient care and staff are reported.

Consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis in ruminants.

The Standards for Reporting of Diagnostic Accuracy (STARD) statement (www.stard-statement.org) was developed to encourage complete and transparent reporting of key elements of test accuracy studies in human medicine. The statement was motivated by widespread evidence of bias in test accuracy studies and the finding that incomplete or absent reporting of items in the STARD checklist was associated with overly optimistic estimates of test performance characteristics. Although STARD principles apply broadly, specific guidelines do not exist to account for unique considerations in livestock studies such as herd tests, potential use of experimental challenge studies, a more diverse group of testing purposes and sampling designs, and the widespread lack of an ante-mortem reference standard with high sensitivity and specificity. The objective of the present study was to develop a modified version of STARD relevant to paratuberculosis (Johne's disease) in ruminants. Examples and elaborations for each of the 25 items were developed by a panel of experts using a consensus-based approach to explain the items and underlying concepts. The new guidelines, termed STRADAS-paraTB (Standards for Reporting of Animal Diagnostic Accuracy Studies for paratuberculosis), should facilitate improved quality of reporting of the design, conduct and results of paratuberculosis test accuracy studies which were identified as "poor" in a review published in 2008 in Veterinary Microbiology.

Mycobacterium kansasii infection in a bontebok (Damaliscus pygaragus dorcas) herd: diagnostic challenges in differentiating from the Mycobacterium tuberculosis complex.

Two adult female bontebok (Damaliscus pygarus dorcas) were euthanized because of signs of pneumonia and weakness (case 1), and a nonresponsive lameness with draining fistula (case 2). Necropsy findings were similar in both cases and consisted of disseminated granulomatous lesions in the liver, kidneys, spleen, lungs, pleural surfaces, and multiple lymph nodes. Mycobacterium kansasii was isolated from both cases after multiple attempts on a variety of samples by two laboratories. The remaining four animals in the herd were tested for antibody responses using the Chembio ElephantTB STAT-PAK, DPP VetTB kits, and multi-antigen print immunoassay (MAPIA), for immune reaction using the intradermal tuberculin test, and by tracheal wash cultures, and thoracic radiographs. Banked serum samples collected in 2005 and obtained from the original institution, revealed 1/9 (11.11%) seropositive animals using the three immunoassays. Retesting the current herd in 2008 showed 2/6 (33.33%) seropositive animals by the three tests, with MAPIA demonstrating antibody reactivity to MPB83 and MPB70 proteins. Inconsistent intradermal tuberculin test results, cross-reactivity in serologic assays designed for tuberculosis detection, difficulty in obtaining definitive identification by culture, and inability to identify a source of infection created challenges in distinguishing the atypical mycobacteriosis due to M. kansasii from the initially suspected tuberculous infection in this herd. Owing to regulatory considerations, differences in host-to-host transmission, and source of infection between Mycobacterium tuberculosis complex and nontuberculous mycobacteria, correct diagnosis is crucial for management of these diseases in wildlife species.

Tracing the origins of Mycobacterium bovis tuberculosis in humans in the USA to cattle in Mexico using spoligotyping.

OBJECTIVES: To compare genotypes of Mycobacterium bovis strains from humans in Southern California with genotypes of M. bovis strains in cattle in Mexico and the USA to explore the possible origins of human infections. METHODS: We conducted a descriptive analysis of M. bovis genotypes from a binational population of humans and cattle using spacer oligonucleotide typing (spoligotyping). RESULTS: One hundred six human M. bovis spoligotypes were compared to spoligotypes from 496 Mexican cattle and 219 US cattle. Twelve spoligotype patterns were identified among human cases and 126 spoligotype patterns were detected in cattle. Over 91% (97/106) of the human M. bovis isolates had spoligotypes that were identical to those found in Mexican cattle. Four human cases had spoligotypes that matched both cattle born in Mexico and in the USA. Nine human cases had spoligotypes that did not match cattle born in Mexico or the USA. CONCLUSIONS: Our data indicate that the population of M. bovis strains causing human TB disease in Southern California is closely related to the M. bovis strain population found in Mexican cattle and supports existing epidemiological evidence that human M. bovis disease in San Diego likely originated from Mexican cattle.