Transtracheal Aspiration Research Articles

Microbial populations vary between the upper and lower respiratory tract, but not within biogeographic regions of the lung of healthy horses

Understanding normal microbial populations within areas of the respiratory tract is essential, as variable regional conditions create different niches for microbial flora, and proliferation of commensal microbes likely contributes to clinical respiratory disease. The objective was to describe microbial population variability between respiratory tract locations in healthy horses. Samples were collected from four healthy adult horses by nasopharyngeal lavage (NPL), transtracheal aspirate (TTA), and bronchoalveolar lavage (BAL) of six distinct regions within the lung. Full-length 16S ribosomal DNA sequencing and microbial profiling analysis was performed. There was a large amount of diversity, with over 1797 ASVs identified, reduced to 94 taxa after tip agglomeration and prevalence filtering. Number of taxa and diversity were highly variable across horses, sample types, and BAL locations. Firmicutes, proteobacteria, and actinobacteria were the predominant phyla. There was a significant difference in richness (Chao1, p = 0.02) and phylogenetic diversity (FaithPD, p = 0.01) between NPL, TTA, and BAL. Sample type (p = 0.03) and horse (p = 0.005) contributed significantly to Bray-Curtis compositional diversity, while Weighted Unifrac metric was only affected by simplified sample type (NPL and TTA vs BAL, p = 0.04). There was no significant effect of BAL locations within the lung with alpha or beta diversity statistical tests. Overall findings support diverse microbial populations that were variable between upper and lower respiratory tract locations, but with no apparent difference in microbial populations of the six biogeographic regions of the lung, suggesting that BAL fluid obtained blindly by standard clinical techniques may be sufficient for future studies in healthy horses.

Mesenchymal Stem Cells Reduce the Extracellular Mitochondrial DNA-Mediated TLR9 Activation in Neonatal Hyperoxia-Induced Lung Injury.

Mitochondrial DNA (mtDNA) released from dead or injured cells can activate inflammation, and mesenchymal stem cell (MSC) transplantation can reduce inflammation and injury. However, it has not been tested whether the release of mtDNA can be reduced by MSC transplantation. We hypothesized that the level of extracellular mtDNA would be increased after hyperoxia-induced lung injury but reduced after lung injury attenuation by MSC therapy in our newborn rat model. In an in vitro study using a rat lung epithelial L2 cell line, we found that the level of extracellular mtDNA was significantly increased with H2O2-induced cell death but reduced after MSC co-incubation. In an in vivo study, we confirmed that the levels of cell death, extracellular mtDNA, and inflammatory cytokines were significantly increased in hyperoxic newborn rat lungs but reduced after MSC transplantation. The levels of extracellular mtDNA were significantly and positively correlated with the levels of the inflammatory cytokines. The TLR9/MyD88/NF-κB pathway, which is activated by binding to mtDNA, was also significantly upregulated but downregulated after MSC transplantation. We found a significant positive correlation between inflammatory cytokines and extracellular mtDNA in intubated neonates. The levels of inflammatory cytokines and extracellular mtDNA changed over time in a similar pattern in transtracheal aspirate samples from intubated neonates. In conclusion, increased levels of extracellular mtDNA are associated with increased inflammation in hyperoxia-induced lung injury, and attenuation of lung inflammation by MSC therapy is associated with reduced levels of extracellular mtDNA.

Resistance patterns of bacterial pathogens causing lower respiratory tract infections: Aleppo-Syria.

This study aimed to scan the bacterial spectrum causing LRTIs, their susceptibility profile and patient related risk factors. Two hundred sixty-eight specimens from LRTIs suspected patients attending University Hospital were collected. Specimens included bronchial washings, transtracheal aspiration samples and sputum. After appropriate culture and identification tests, susceptibility test was done using minimum inhibitory concentration method. Data were collected from patients for further analysis. of total specimens, 150 showed positive culture results (Acinetobacter baumannii, Pseudomonas aeruginosa, Citrobacter koseri, Escherichia coli, Klebsiella pneumonia, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Streptococcus pneumonia and Candida spp.). The antibiogram showed high resistance among all bacterial isolates against most antibiotics. Good susceptibility rates were shown to colistin in Gram-negative group and piperacillin\tazobactam in Gram-positive group. Trimethoprim\sulfamethoxazole showed good susceptibility results in both groups. Many factors showed correlation with LRTIs such as age (P=0.004), smoking (P=0.049), residency (P=0.043), hypertension (P=0.012), lung chronic disease (P=0.007) and cancer (P=0.048). The leading cause of LRTIs in our study were A. baumannii and P. aeruginosa which both are very troublesome pathogens and multidrug resistant frequency was alarming. Random empirical antibiotic using can highly lead to increased resistance. Further care must be taken after patients with risk factors, and adjustments should be done to those modifiable factors.

9 Respiratory microbiota in horses are individual-specific rather than biogeographically variable

Respiratory disease in horses is associated with transportation, aspiration of oral contents, and primary infectious diseases, and has significant implications for both horse welfare and economic stability of equine industry. Regional conditions within the respiratory tract vary widely in temperature, nutrient availability, pH, and oxygen tension, creating different niches for microbial flora, some of which may not be identified by bacteriologic culture. Proliferation of commensal microbes likely contributes to initiation and progression of clinical disease. Understanding normal microbial populations is essential to investigating dysbiosis in the development of infectious respiratory disease. However, microbial populations within the equine lung have not been investigated with next generation sequencing technologies. Therefore, the study objective was to describe microbial population variability between respiratory tract locations in healthy horses. Samples were collected from 4 healthy adult horses, 2 mares and 2 geldings, aged 10–25 years, Thoroughbred, Standardbred, and Warmblood (2) breeds. Additional inclusion criteria were no history of respiratory or systemic disease within 2 mo of study, and no transportation within 1 week of sample collection at the University of Illinois Veterinary Teaching Hospital. Samples were collected by nasopharyngeal lavage (NPL) and transtracheal aspirate (TTA) premortem, and bybronchoalveolar lavage (BAL) of 6 distinct regions within the lung immediately post-mortem. Microbial DNA was extracted and full-length 16S ribosomal DNA sequencing was performed, followed by microbial profiling analysis with TADA Nextflow and R. There was a large amount of diversity, with over 1800 taxa identified, reduced to 160 taxa after prevalence filtering. The number of taxa and diversity were highly variable across sample locations. Actinobacteria, proteobacteria, and firmicutes were the predominant phyla. There was no significant difference in α or β diversity between the 3 sampling locations (NPL, TTA, BAL). When NPL and TTA were combined, there was a significant difference in α diversity compared with lung for Chao1, ACE and PD indices. There was significant difference in β diversity between horses. Overall, microbiota in respiratory samples of heathy horses were highly variable. Taxa were more similar between regions within the same horse, than between the same region of different horses, suggesting that respiratory microbiota are unique to individuals. These findings do not support presence of a core respiratory microbiome across individuals.

Comparison of pathogenic bacteria in the upper and lower respiratory tracts of cattle either directly transported to a feedlot or co-mingled at auction markets prior to feedlot placement.

Bacterial bronchopneumonia (BP) has been associated with purchasing cattle through auction markets. However, whether auction markets are a source of BP-associated bacterial pathogens is unknown. This study evaluated prevalence, antimicrobial susceptibility, and genetic relatedness (using pulsed-field gel electrophoresis, PFGE) of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from cattle either transported to an auction market prior to feedlot placement (AUC), or directly to a feedlot from a farm (RANC). Two groups of cattle were enrolled (N = 30 per group) from two separate farms with 15 animals from an individual farm designated as AUC or RANC. Deep nasal swab (DNS) and trans-tracheal aspirates (TTA) were collected on day 0 at weaning (T0) and on day 2 at on-arrival processing at the feedlot (T1). The DNS were also collected on day 9 (T2) and day 30 (T3) after arrival at the feedlot. In both TTA and DNS, prevalence of bacteria did not differ between AUC and RANC groups (P > 0.05). None of the bacteria isolated at T0 were resistant to antimicrobials and diversity of all bacteria was greatest at T0 and T1. In Group 1 cattle, 100% of P. multocida isolated at T2 and T3 were multi-drug resistant. These isolates were highly related (>90%) according to PFGE, with most being clones. Though limited in size, results for animals evaluated in this study suggested that auction markets were not a major source of resistant BP pathogens, however, horizontal transmission of a multi-resistant strain of P. multocida occurred in a feedlot. Spread of resistant P. multocida was likely due to the selective pressures imposed by feedlot antimicrobial use and encoded resistance by the bacteria.

Changes in Respiratory Pathogens before and after the COVID-19 Pandemic (2018-2021).

Objective This study is aimed at investigating the pattern of change occurring in respiratory pathogens before and after the outbreak of COVID-19, a type of viral pneumonia for which a pandemic was declared (March 2020). The results were analyzed by gender and age to identify the association between personal hygiene and prevention of infection by respiratory pathogens. Methods A retrospective analysis was performed on 39,814 sputum, bronchial aspirate, and transtracheal aspirate samples obtained from 15,398 patients visiting a university hospital, located in Chungcheongnam-do, South Korea, between January 2018 and December 2021. From 4,454 patients whose samples were culture positive for bacteria, 6,389 strains were isolated and further cultured. Results The mean age of the outpatients with respiratory pathogens was 66.2 years, and the comparison of the culture test results by gender showed that 64.9% (2,892/4,454) were male and 35.1% (1,562/4,454) were female. Compared to the pre-COVID-19 pandemic period, the number of outpatients with a request for respiratory microbial cultures after the onset of the pandemic was reduced by 20.7% and the number of outpatients with a positive culture result was reduced by 23.0%. The number of respiratory samples received was reduced by 6.7% after the pandemic, while the sample positive rate was reduced by 18.3%. Among the isolated microbial strains, there was a significant decrease of 43.1% for the Acinetobacter baumannii complex, 60.5% for Streptococcus pneumoniae, 67.2% for Haemophilus influenzae, and 78.1% for Moraxella catarrhalis when compared with pre-COVID-19 levels. The distribution of respiratory microbial strains by age group showed that the highest percentage of isolated strains was in patients in their 70s. Conclusions The improvements in personal hygiene due to the COVID-19 pandemic exerted a substantial influence on the pattern of change in other common respiratory microorganisms, which highlights the importance of personal hygiene management in the prevention of respiratory infections.

Hyponatremia in horses with septic pneumopathy.

BackgroundHyponatremia is common in horses with bacterial pleuropneumonia, but no further characterization of this abnormality has been reported.ObjectivesDescribe admission plasma sodium concentration ([Na]) in horses with septic pneumopathy and evaluate any association of plasma [Na] with markers of systemic inflammation.AnimalsMedical records of horses >1 month of age that between 2008 and 2021 had a transtracheal aspirate (TTA) performed, abnormal TTA cytology, positive TTA culture, pulmonary disease on ultrasonography, radiography or both, and plasma [Na] assessed by direct ion‐selective‐electrode (dISE). Horses with concurrent diarrhea or azotemia were excluded.MethodsClinical and clinicopathological variables of interest between hypo‐ and normonatremic horses were compared. Spearman correlation and Fisher exact tests were used to identify significant associations (P < .05).ResultsTwenty of 35 horses had hyponatremia (median, 132 mmol/L; 25‐75th interquartile range [IQR], 129.7‐133.1 mmol/L; reference range, 134.2‐138.4 mmol/L). A higher proportion of horses with systemic inflammatory response syndrome (SIRS) had hyponatremia (P = .01). Hyponatremic patients had higher mean plasma fibrinogen concentration (461 ± 160.5 mg/dL; P = .01) and higher rectal temperature (38.8 ± 0.7°C; P = .02) than normonatremic horses. Negative correlations were found between plasma [Na] and fibrinogen (P = .001; ρ = −0.57) concentrations and between plasma [Na] and rectal temperature (P = .001; ρ = −0.51). Presence or absence of pleural effusion did not influence severity of hyponatremia. Mean duration of hospitalization was longer (P = .04) in hyponatremic horses (9.8 ± 6.6 days).Conclusions and Clinical ImportanceHyponatremia at admission is associated with the presence of inflammation, SIRS, and with longer duration of hospitalization.

Early Immunomodulatory Effects of Different Natural Surfactant Preparations in Preterms With Respiratory Distress.

BackgroundRespiratory distress syndrome (RDS) is the most common respiratory disease in premature infants. Exogenous natural surfactant preparations are used in the treatment of RDS. In recent years, it has become increasingly evident that surfactant plays an immunoregulatory role.ObjectivesThe aim of this study was to evaluate cytokine and chemokine response following three different regimens of natural surfactant treatment in preterm newborns with RDS.MethodsPremature newborns below 32 weeks of gestation who were intubated for RDS and given early surfactant rescue therapy were included in the study. Newborns were randomly divided into three groups and Beractant 100 mg/kg (B-100), Poractant alfa 100 mg/kg (Pα-100) and Poractant alfa 200 mg/kg (Pα-200) were administered intratracheally. Blood samples and transtracheal aspirates (TA) were collected just before and 4–6 h after the surfactant treatment. Total eosinophil count, inducible T Cell alpha chemoattractant (ITaC), macrophage inflammatory protein 3 beta (MIP3b), interleukins (IL) 5, 8, 9, 10, 13, immunoglobulin E (IgE), interferon gamma (IFN-γ), eotaxin and tumor necrosis factor beta-1 (TGF-β1) were measured from blood and tracheal aspirate samples.ResultsA total of 45 infants, 15 in each group, were included in the study. Mean gestational age, birth weight, antenatal, demographic and clinical characteristics of the study groups were similar. IFNγ concentration and eosinophil counts in TA decreased after surfactant replacement in all groups, especially in the infants treated with Pα-100 and Pα-200. Eotaxin, TGF beta and IL-8 concentrations in TA increased significantly in the infants treated with Pα-100 and Pα-200. IL-9 levels in TA decreased in the B-100 group but increased in the Pα-100 and Pα-200 groups. Blood levels of cytokines and chemokines showed significantly decreased levels of ITaC and MIP3b only in the B-100 group, but no significant change was observed in the Pα-100 and Pα-200 groups.ConclusionIn our study, the different immunomodulatory effects of natural surfactant preparations on newborn lung is proven. We found that Poractant α, one of the natural surfactant preparations, shifted the lung immune system toward TH2.

BKC-2, a New BKC Variant Detected in MCR-9.1-Producing Enterobacter hormaechei subsp. xiangfangensis.

We characterized a multidrug-resistant (MDR) Enterobacter spp. isolate highlighting the genetic aspects of the antimicrobial resistance genes. An Enterobacter spp. isolate (Ec61) was recovered in 2014 from a transtracheal aspirate sample from a patient admitted to a Brazilian tertiary hospital and submitted to further microbiological and genomic characterization. Ec61 was identified as Enterobacter hormaechei subsp. xiangfangensis strain ST451, showing an MDR profile and the presence of genes codifying the new β-lactamase variants BKC-2 and ACT-84 and the mobile colistin resistance gene mcr-9.1.

1224. Investigation of Infectious Etiologies in the Lower Respiratory Tract from Pediatric Patients with Unexpected Cardiopulmonary Deterioration using Next-Generation Sequencing

BackgroundIn pediatric patients, unexpected cardiopulmonary deterioration with or without following cardiopulmonary arrest (CPA) are rare events, but can be caused by any of several etiologies, including infectious diseases. The most common cause of out-of-hospital CPA in children ≤12 years old was sudden infant death syndrome (SIDS), whereas infectious diseases were responsible for approximately 10% of the CPA cases. However, the role of infection may have been underestimated as triggers of SIDS or CPA. This study aimed to investigate the infectious etiologies in pediatric patients with unexpected cardiopulmonary deterioration using next-generation sequencing (NGS).MethodsA total of 16 pediatric patients who were admitted to the pediatric intensive care unit with unexpected cardiopulmonary deterioration with or without following CPA were enrolled. Ten bronchoalveolar fluid (BALF) and six transtracheal aspirates (TTA) samples obtained in the acute phase were used to prepare NGS libraries. The libraries were sequenced on HiSeq and analyzed using metagenome analysis tools.ResultsIn ten of 16 patients, one or more bacterial/viral pathogens were detected in the BALF or TTA specimens using NGS. Compared to the conventional culture and viral antigen test results, an additional 6 bacterial (e.g., Chlamydia trachomatis) and 4 viral pathogens (e.g., coxsackievirus A6 and human coronavirus NL63) were identified by NGS in four of ten patients in whom no causative pathogen had been identified by conventional culture and viral antigen tests. A summary of the detected pathogens is listed in Table 1. Notably, sequencing results allowed us to define genotypes for all of the detected viruses in a single NGS assay per patient. Furthermore, based on phylogenetic analysis of the VP1 region, the coxsackievirus A6 strain detected in this study belongs to lineage E2 and harbors an amino acid change (T283A), a substitution that has potential to cause severe illness.Table 1 ConclusionOur results suggest that viral and bacterial infection are common triggers in unexpected cardiopulmonary deterioration in pediatric patients. NGS has the potential to contribute to the clarification of the etiology of pediatric critical illness.Disclosures All Authors: No reported disclosures

First report of pulmonary disease associated with Nicoletella semolina in a horse in New Zealand

ABSTRACT Case history: A 9-year-old warmblood gelding with a history of chronic intermittent tachypnoea and dyspnoea was presented for evaluation and removal of a mass on the left side of the neck. A fibrous mass adherent to the left jugular vein developed and was removed surgically 6 weeks later, at which time the owner requested an evaluation of the cause of the persistent respiratory signs first noted on primary admission. Clinical findings and treatment: Clinical findings included coarse lung sounds on thoracic auscultation, tracheal wheeze, and an abnormal trans-tracheal aspirate. These findings, in addition to the results of ultrasonographic imaging of the thorax and transtracheal cytology, were suggestive of bacterial bronchopneumonia. Initial antimicrobial therapy included I/M 22 mg/kg procaine penicillin every 12 hours and I/V 6.6 mg/kg gentamicin sulphate every 24 hours. The horse’s clinical signs improved within 36 hours. It was discharged after 6 days, and at the owner's request antimicrobial therapy was changed to 25 mg/kg trimethoprim/sulphadimidine to be given orally every 12 hours for 10 days. One month later, the horse had recovered and there were no further complications reported by the owner except for an occasional cough while grazing Laboratory findings: Bacterial culture of transtracheal wash fluid resulted in the isolation of Nicoletella semolina as the sole organism, later confirmed by genotyping. Attempts to subculture the organism for antimicrobial susceptibility testing were unsuccessful. Diagnosis: Infectious bronchopneumonia associated with Nicoletella semolina Clinical relevance: Further work is required to determine whether N. semolina is acting as an opportunistic commensal of the equine respiratory tract or a primary pathogen. However, this article reports the first instance in New Zealand of an association between the presence of this organism and respiratory disease in a horse.

Comprehensive Detection of Candidate Pathogens in the Lower Respiratory Tract of Pediatric Patients With Unexpected Cardiopulmonary Deterioration Using Next-Generation Sequencing.

Next-generation sequencing has been applied to the investigation of microorganisms in several clinical settings. We investigated the infectious etiologies in respiratory specimens from pediatric patients with unexpected cardiopulmonary deterioration using next-generation sequencing. Retrospective, single-center, observational study. Tertiary care, a children's hospital. The study enrolled a total of 16 pediatric patients with unexpected cardiopulmonary deterioration who were admitted to the PICU. Ten bronchoalveolar lavage fluid and six transtracheal aspirate samples were analyzed. None. RNA libraries were prepared from specimens and analyzed using next-generation sequencing. One or more bacterial/viral pathogens were detected in the bronchoalveolar lavage fluid or transtracheal aspirate specimens from 10 patients. Bacterial and viral coinfection was considered in four cases. Compared with the conventional culture and viral antigen test results, an additional six bacterial and four viral pathogens were identified by next-generation sequencing. Conversely, among 18 pathogens identified by the conventional methods, nine pathogens were detected by next-generation sequencing. Candidate pathogens (e.g., coxsackievirus A6 and Chlamydia trachomatis) were detected by next-generation sequencing in four of 10 patients in whom no causative pathogen had been identified by conventional methods. Our results suggest that viral and bacterial infections are common triggers in unexpected cardiopulmonary deterioration in pediatric patients. Next-generation sequencing has the potential to contribute to clarification of the etiology of pediatric critical illness.

Methods of antemortem sampling for identification of microbial agents in bovine respiratory disease (BRD)

Although bovine respiratory disease (BRD) can often be managed satisfactorily without diagnosis of microbial agents, when presumptive management is unsuccessful, identification of viruses or bacteria may reveal unexpected contributors, or agents for which a change in vaccination strategy or antimicrobial may be appropriate. The most common and feasible techniques for field use include nasal swabs, guarded nasopharyngeal swabs (NPS), transtracheal aspiration, and non-endoscopic bronchoalveolar lavage (BAL). Nasal swabs or NPS are ideal for rapidly sampling large numbers of cattle; evidence suggests that testing these for viruses or bacteria reliably represents the agents in the lower respiratory tract at the group level. If only 1 or a small number of animals are to be sampled, the tracheal aspirate or BAL may provide a more reliable result. Recent vaccination with modified-live viral (MLV) vaccines can cause false positive results by any method, thus sampling should not be carried out within 1 month of MLV vaccination. Paired serology can be useful for diagnosis of viral agents, but serologic tests for bacterial BRD agents are not readily available in diagnostic laboratories. Paired serology can be difficult to interpret in calves with maternal antibody, or in recently vaccinated cattle.

Microbiology of Aspiration Pneumonia

The number of patients with pneumonia has been increasing as the population ages, and most fatal pneumonia cases are the elderly with aspiration pneumonia. Although aspiration pneumonia leads to poor short- and long-term prognosis, there have been no practical ways to diagnose it precisely. Persistent subclinical aspiration without any subjective symptoms is problematic in clinical practice in patients with aspiration pneumonia, and physicians can only use aspiration risks such as brain infarction to diagnose aspiration pneumonia. Anaerobes have been believed to be major causative pathogens in aspiration pneumonia, based on data from the 1970's. In relation to these data, Marik insisted that there is a possible overestimation of anaerobes because 1) the sampling of microbiologic specimens was in the late phase in the course of the illness, especially frequently after developing complications such as abscesses, necrotizing pneumonia, or empyema thoracis; 2) the organisms recovered by percutaneous transtracheal aspiration (PTA) sampling could have been contaminated by the aspiration of oropharyngeal flora during the PTA procedure or colonized in the trachea; and 3) many of the patients had chronic alcoholism or were under general anesthesia. In addition, 4) oral care was not common in the 1970s, and 5) the patients in these reports were relatively young. Molecular biological approaches using the 16S ribosomal RNA (rRNA) gene have recently been used, and have enabled us to detect more exact pathogens compared to conventional bacterial culture. Using the method with the detection of the 16S rRNA gene, we evaluated the bacterial phylotypes in bronchoalveolar lavage fluid in patients with aspiration pneumonia and found that oral streptococci were the most detected phylotypes (31.0%), while anaerobes were only 6.0%. Our results suggest that oral streptococci are important, and anaerobes may have been overestimated as causative pathogens in patients with aspiration pneumonia.

Plasmid analysis of Escherichia coli isolates from South Korea co-producing NDM-5 and OXA-181 carbapenemases

Recently, Escherichia coli isolates co-producing New Delhi metallo-β-lactamase (NDM)-5 and oxacillinase (OXA)-181 were identified in a tertiary-care hospital of South Korea. Isolate CC1702–1 was collected from urine in January 2017 and isolate CC1706-1 was recovered from a transtracheal aspirate of a hospitalized patient in May 2017. Carbapenemase genes were identified by multiplex PCR and sequencing, and whole genome sequencing was performed subsequently using the PacBio RSII system. Both E. coli isolates belonged to the same clone (ST410) and were resistant to all β-lactams including carbapenems. We obtained whole plasmid sequences of the isolates: pCC1702-NDM-5 from CC1702-1 and pCC1706-NDM-5 and pCC1706-OXA-181 from CC1706-1. The two E. coli isolates belonged to the same clone (ST410) and they were completely resistant to all β-lactams, as well as carbapenems. Two blaNDM-5-harboring plasmids belonged to the same incompatibility group, IncFIA/B, and consisted of 79,613 bp and 111,890 bp with 87 and 130 coding sequences, respectively. The genetic structures of the two blaNDM-5-bearing plasmids, which were distinct from the blaNDM-5-bearing plasmids from the Klebsiella pneumoniae isolates previously transmitted from the United Arab Emirates (UAE) to South Korea, differed from each other. While pCC1702-NDM-5 showed high degree of identity with the plasmid from a multidrug-resistant isolate of Citrobacter fruendii P5571 found in China, pCC1706-NDM-5 was very similar to the plasmid from a multidrug-resistant isolate of E. coli AMA1176 found in Denmark. pCC1706-OXA-181, which was a 51 kb, self-transmissible IncX3 plasmid, was identical to the E. coli plasmids pAMA1167-OXA-181 from Denmark and pOXA-181-WCHEC14828 from China. Plasmids harboring blaNDM-5 in E. coli isolates might not be transferred from K. pneumoniae isolates co-producing NDM-5 and OXA-181. They probably originated from multiple sources.

Clinical presentation and management of African horse sickness in two dogs

A 10-month-old, spayed, female beagle (case 1) and an unrelated two-year-old, intact, female labrador retriever (case 2), both living in Pretoria, South Africa, presented individually on separate occasions with acute...

Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle

The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.

Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia

Specific nasopharyngeal bacterial communities can provide colonization resistance against respiratory pathogens in cattle. However, the role of bacterial communities of the lower airways in respiratory health remains largely unknown. Therefore, our objective was to compare nasopharyngeal and tracheal bacterial communities between healthy feedlot cattle and those with bronchopneumonia (BP). Deep nasal swabs and trans-tracheal aspiration samples were collected from steers with (n = 60) and without (n = 60) BP at 4 feedlots in Western Canada. After DNA extraction, 16S rRNA gene (V4) was amplified and sequenced. Alpha-diversity analysis revealed a lower bacterial diversity in the nasopharynx and trachea of steers with BP compared to healthy pen-mates. Bacterial communities present within the airways clustered into 4 distinct metacommunities that were associated with sampling locations and health status. Metacommunity 1, enriched with Mycoplasma bovis, Mannheimia haemolytica and Pasteurella multocida, was dominant in the nasopharynx and trachea of steers with BP. In contrast, metacommunity 3, enriched with Mycoplasma dispar, Lactococcus lactis and Lactobacillus casei, was mostly present in the trachea of healthy steers. Metacommunity 4, enriched with Corynebacterium, Jeotgalicoccus, Psychrobacter and Planomicrobium, was present in the nasopharynx only. Metacommunity 2, enriched with Histophilus somni, Moraxella and L. lactis, was present in both healthy and sick steers, but was primarily detected in one feedlot. We concluded that distinct bacterial metacommunities inhabited the nasopharynx and trachea of healthy feedlot cattle and those with BP. Because L. lactis and L. casei can inhibit M. haemolytica growth in vitro, their presence in healthy steers may have provided colonization resistance against bacterial respiratory pathogens.

Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection

BackgroundInformation on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. The detection of MERS-CoV sub-genomic mRNAs indicates that the virus is replicative. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. MethodsUpper and lower respiratory samples were obtained from 17 MERS-CoV-infected patients. MERS-CoV sub-genomic mRNA was detected by reverse transcription PCR (RT-PCR) and MERS-CoV genomic RNA by real-time RT-PCR. ResultsIn sputum and transtracheal aspirate, sub-genomic mRNA was detected for up to 4 weeks after symptoms developed, which correlated with the detection of genomic RNA. In oropharyngeal and nasopharyngeal swab specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. ConclusionsThese findings suggest that MERS-CoV does not replicate well in the upper respiratory tract.

ERIC-PCR Genotyping of Acinetobacter baumannii Isolated from Different Clinical Specimens.

Background:Acinetobacter baumannii is a major cause of hospital care-acquired infections, and this bacterium poses a significant challenge to health care worldwide. At King Fahd Hospital of the University (KFHU), Al Khobar, Saudi Arabia, there had been a significant increase in the number of cases of A. baumannii infections.Objective:The objective of this study was to determine the clonal relationship between A. baumannii collected from different specimens of patients admitted to KFHU using the enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) fingerprinting method.Materials and Methods:A. baumannii strains were isolated from a total of 59 specimens from inpatients admitted to KFHU between January and September 2014. These specimens were mainly collected from wound, rectal and throat swabs and transtracheal aspiration. ERIC-PCR fingerprinting was used to determine the clonal relationship between the different isolated strains.Results:Using ERIC-PCR fingerprinting genotype analysis, 51 strains of A. baumannii were clustered into seven groups, while the remaining 8 were single strains. The genetic relatedness of A. baumannii isolated from admitted patients was high, indicating cross-transmission within the hospitalized patients.Conclusion:This study found that the increase in the incidence of A. baumannii in patients at KFHU was likely due to the spread of seven epidemic clones, thereby highlighting the need for intensifying the infection control measures to prevent nosocomial transmission of A. baumannii. These results also demonstrate that ERIC-PCR is a reliable and rapid method for studying the clonal similarity between A. baumannii isolated from different clinical specimens.