Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia.

BACKGROUND: Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE: To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS: Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS: Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS: Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.

Identification of four patients with colistin-resistant Escherichia coli containing the mobile colistin resistance mcr-1 gene from a single health system in Michigan.

Clinical Enterobacteriacae isolates with a colistin minimum inhibitory concentration (MIC) ≥4 mg/L from a United States hospital were screened for the mcr-1 gene using real-time polymerase chain reaction (RT-PCR) and confirmed by whole-genome sequencing. Four colistin-resistant Escherichia coli isolates contained mcr-1. Two isolates belonged to the same sequence type (ST-632). All subjects had prior international travel and antimicrobial exposure.

Safety and Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Highly Pathogenic Organisms.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods, including the direct, on-plate formic acid, and ethanol/formic acid tube extraction methods, were evaluated for their ability to render highly pathogenic organisms nonviable and safe for handling in a biosafety level 2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight-laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their in vitro diagnostic (IVD), research-use-only, and Security-Relevant databases, as applicable, to accurately identify these agents. Forty-six distinct strains of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia mallei, Burkholderia pseudomallei, Clostridium botulinum, Brucella melitensis, Brucella abortus, Brucella suis, and Brucella canis were extracted and distributed to participating laboratories for analysis. A total of 35 near-neighbor isolates were also analyzed.

High-throughput vector-borne disease environmental surveillance by polymerase chain reaction according to international accreditation requirements.

Although vector-borne diseases are specific to the region of the host, there is a necessity for surveillance or reference laboratories to perform standardized, high-throughput testing capable of meeting the needs of a changing military environment and response efforts. The development of standardized, high-throughput, semiquantitative real-time and reverse transcription real-time polymerase chain reaction (PCR) methods allows for the timely dissemination of data to interested parties while providing a platform in which long-term sample storage is possible for the testing of new pathogens of interest using a historical perspective. PCR testing allows for the analysis of multiple pathogens from the same sample, thus reducing the workload of entomologists in the field and increasing the ability to determine if a pathogen has spread beyond traditionally defined locations. US Army Public Health Command Region-Europe (USAPHCR-Europe) Laboratory Sciences (LS) has standardized tests for 9 pathogens at multiple life stages. All tests are currently under international accreditation standards. Using these PCR methods and laboratory model, which have universal Department of Defense application, the USAPHCR-Europe LS will generate quality data that is scientifically sound and legally defensible to support force health protection for the US military in both deployed and garrison environments.

Prevalence of Clostridium difficile toxin genes in the feces of veal calves and incidence of ground veal contamination.

A study was conducted in two parts to determine the prevalence of toxigenic Clostridium difficile in veal calves and retail meat. The first part of the study focused on the veal production continuum (farm to abattoir). Fifty calves from 4 veal herds (n=200) were followed for 18-22 weeks from the time of arrival on the veal farm to the time of slaughter. Fecal samples were collected from calves every 4-6 weeks. Half of the calves included in the study (n=100) were followed to the abattoir where carcass swabs were collected post slaughter. Fecal samples and carcass swabs were screened for genes encoding C. difficile toxins TcdA, TcdB, and CDT by using real-time polymerase chain reaction (PCR). Carcass swabs were also screened for toxigenic C. difficile by using traditional culture methods. In the second part of the study, ground veal products (n=50 samples) purchased from local grocery stores were examined for toxigenic C. difficile by using real-time PCR and traditional culture methods. Fecal samples from 56 of 200 (28%) calves tested positive for C. difficile toxin genes at least once over the course of the study. Calf age (p=0.011) influenced prevalence of C. difficile toxin genes in calf feces. Toxin genes of C. difficile were detected in one carcass swab by multiplex real-time PCR only. Toxigenic C. difficile was detected by PCR and culture in four (8%) and three (6%) ground veal samples, respectively. The findings of the study reveal that toxigenic C. difficile was most prevalent in veal calves (12%) just before slaughter, although viable toxigenic C. difficile was not recovered from veal carcasses. On the contrary, viable toxigenic C. difficle was recovered from 6% retail meat, thus suggesting that contamination occurs either during or after veal fabrication.

In vitro antimicrobial inhibition of Mycoplasma bovis isolates submitted to the Pennsylvania Animal Diagnostic Laboratory using flow cytometry and a broth microdilution method.

Mycoplasma bovis is an important pathogen of cattle, causing mastitis, pneumonia, conjunctivitis, otitis, and arthritis. Currently there are only a few reports of sensitivity levels for M. bovis isolates from the United States. Mycoplasma bovis isolates submitted to the Pennsylvania Animal Diagnostic Laboratory between December 2007 and December 2008 (n = 192) were tested for antimicrobial susceptibility to enrofloxacin, erythromycin, florfenicol, spectinomycin, ceftiofur, tetracycline, and oxytetracycline using a broth microdilution method. The most effective antimicrobials against M. bovis determined by using the broth microdilution method were florfenicol, enrofloxacin, and tetracycline with minimum inhibitory concentration (MIC) ranges of 2-32 µg/ml, 0.1-3.2 µg/ml, and 0.05 to >12.8 µg/ml, respectively. Spectinomycin, oxytetracycline, and tetracycline showed a wide-ranging level of efficacy in isolate inhibition with broth microdilution with MIC ranges of 4 to >256 µg/ml, 0.05 to >12.8 µg/ml, and 0.05 to >12.8 µg/ml, respectively. A significant difference in the susceptibility levels between quarter milk and lung isolates was found for spectinomycin. When MIC values of a subset of the M. bovis isolates (n=12) were tested using a flow cytometric technique, the MIC ranges of enrofloxacin, spectinomycin, ceftiofur, erythromycin, tetracycline, oxytetracycline, and florfenicol ranges were 0.1-0.4 µg/ml, 4 to >256 µg/ml, >125 µg/ml, >3.2 µg/ml, <0.025 to >6.4 µg/ml, 0.8 to >12.8 µg/ml, and <2-4 µg/ml, respectively. Flow cytometry offers potential in clinical applications due to high-throughput capability, quick turnaround time, and the objective nature of interpreting results.

Blinded, controlled field trial of two commercially available Mycoplasma bovis bacterin vaccines in veal calves.

Mycoplasma bovis is an etiologic agent of pneumonia, arthritis, and otitis in young calves, such as those found in the special-fed veal industry. We conducted a blinded, controlled trial of two commercially available M. bovis bacterin vaccines for the prevention of respiratory disease in calves associated with M. bovis infection. Calves were randomly assigned to a subcutaneous treatment of vaccine A (n=50), adjuvant A (n=50), vaccine B (n=50), or 0.9% sterile saline solution (n=50) beginning at 27 days of age. Upper-respiratory tract colonization was not impacted by vaccination status. Vaccine A significantly reduced the presence of lung lesions (p=0.0325), however there was no significant reduction of M. bovis in lung lesions. Vaccine B did not significantly reduce total lung lesions or M. bovis-specific lung lesions. The relative risk was determined to be 0.56, 1.0, and 1.36 for vaccine A, adjuvant A, and vaccine B, respectively. There was no association between the total specific antibody isotype (IgM, IgG1, IgG2, IgA) concentrations or M. bovis antibodies and the M. bovis-associated morbidity in the veal calves. Under the field conditions of this study, observed vaccine efficacy for vaccine A and vaccine B was 44% and less than 1%, respectively.

Identification of novel small molecule antimicrobials targeting Mycoplasma bovis.

OBJECTIVES: To screen novel small molecule compounds for inhibition of Mycoplasma bovis growth and to characterize their activity in terms of dose-dependency and ability to function in milk. METHODS: Using a tetrazolium salt cytotoxicity assay, 480 natural compounds were screened to determine which of the small molecules have the potential to become therapeutic options for M. bovis prevention and treatment. The dose response was determined in broth culture and in fresh quarter milk for a subset of compounds shown to be capable of inhibiting M. bovis growth. RESULTS: Data suggest that 32 of the 480 compounds tested were able to inhibit growth of M. bovis using a tetrazolium salt assay. Methanesulphonic acid, 3-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyloxy](1S,3R,4R,5R)-1,4,5-trihydroxycyclohexane carboxylic acid, S-carboxymethyl-l-cysteine, l-aspartic acid, dihydrotachysterol, eriodictyol and (+)-α-tocopherol acid succinate were selected for further concentration-dependent studies and testing in fresh quarter milk. Each compound demonstrated a dose response in broth culture and at 3 h and 24 h in fresh quarter milk. CONCLUSIONS: Small molecule natural compounds are capable of inhibiting the growth of M. bovis in both a pleuropneumonia-like organism (PPLO) medium and in fresh quarter milk. Results suggest that the compounds are mycoplasmastatic in a dose-dependent manner. By inhibiting M. bovis, small molecule natural compounds offer the potential for prophylactic or therapeutic use on organic and natural farms as a viable alternative to traditional antimicrobial agents.