Rhodococcus equi—Occurrence in Goats and Clinical Case Report

Background: Rhodococcus equi infection is commonly known in equine medicine to cause frequently fatal rhodococcosis. Infections in other species and people are also reported. Clinical manifestation in goats is relatively similar to horses and humans, but data regarding bacterium prevalence are scarce. Thus, the study aimed to estimate the occurrence of R. equi in goats. Methods: During post mortem examination, submandibular, mediastinal, and mesenteric lymph nodes were collected. Standard methods were used for bacteria isolation and identification. Results: A total of 134 goats were examined, and 272 lymph node samples were collected. R. equi was isolated from four animals. All four isolates carried the choE gene, and one also had traA and pVAPN plasmid genes. Conclusions: To the authors’ best knowledge, this is the first report of R. equi occurrence and genetic diversity in goats. The results may help create a model for treating rhodococcosis in other animal species and assessing the role of meat contamination as a potential source of human infection. This research should be considered a pilot study for further application of the goat as a model of R. equi infection in horses and humans.

Legumes and Nodule Associated Bacteria Interaction as Key Factor for Abiotic Stresses Impact Mitigation

Due to climate change, different soil stresses are increasing continuously and they threat the world food security as they limit crop productivity. Therefore, this chapter aims at integrate information about the interaction between legumes and endophytes which will help to: deep understanding of the endophytes-legume relationship, draw attention to the possibilities to exploit this relationship in soil stress mitigation and unraveling what is need to be addressed in the future. The study reviewed the most recent previous scientific works in the field. For legumes tissue colonization, endophytes almost use the same routs which results in their presence in the same niches. Co-inoculation of these bacteria enhances plant growth directly and indirectly. Some endophytes characterized by stress tolerance which interact with legumes and mitigate the adverse effect of soil stresses like salinity, acidity/alkalinity, drought and heavy metal contamination. To reduce stress and enhance plant growth, legume-associated bacteria produce ACC deaminase and other compounds. The interaction process involves induction and expression of many legume-associated bacteria chromosomal and plasmid genes which indicates that this process is a genetic based. So isolation of stress tolerant legume-associated microbes and identification of the gene related to stress tolerance will aid in production of genetic engineered endophytes adaptive to different stresses. It is concluded that all soil stresses can be addressed by application of stress tolerant endophytes to the soil affected with environmental stresses which is sustainable and low cost approach. To maximize the benefit, searching for indigenous stress tolerant endophytes is recommended.

Effect of pH and Salinity on Lactic Acid Production and Multiplication of Plantaricin Plasmid Genes of Lactobacillus plantarum COY 2906 isolated from Virgin Coconut Oil

Lactic acid bacteria are assumed to act as a biopreservative in virgin coconut oil (VCO) products, even under stress conditions. Lactobacillus plantarum COY 2906 and Lactobacillus sakei were isolated from VCO. L. plantarum COY 2906 showing greater ability than L. sakei to inhibit indicator bacteria and were selected for further study. Under saline stress conditions, L. plantarum COY 2906 did not inhibit E. coli K12 JM109 and showed greater inhibition of B. subtilis than of S. aureus JCM 20624. High saline content reduced lactic acid production, but the copy number of plnA, plnEF, plnN, plnJ and plnK genes associated with plantaricin, was not significantly changed. L. plantarum COY 2906 had its optimum anti-bacterial effect at pH 4.5 – 7.5, while alkaline conditions increased lactic acid production and reduced the multiplication of plantaricin plasmid genes. However, in acidic conditions, the number of plantaricin genes on the plasmid was multiplied. The genes: plnW, plnV, plnU, plnH, plnG, plnE, plnF, plnD, plnC, plnB, plnA, plnR, plnL, plnK, plnJ, plnM, plnN, plnO and plnP were found in the draft genome of L. plantarum COY 2906. This research clearly shows that lactic acid production and multiplication of plantaricin genes are affected by environmental salinity and pH.

Prevalence of Antibiotic-Resistant Escherichia coli Isolated from Swine Faeces and Lagoons in Bulgaria

Antimicrobial resistance (AMR) is a worldwide health problem affecting humans, animals, and the environment within the framework of the “One Health” concept. The aim of our study was to evaluate the prevalence of pathogenic strains of the species Escherichia coli (E. coli), their AMR profile, and biofilm-forming potential. The isolated strains from three swine faeces and free lagoons (ISO 16654:2001/Amd 1:2017) were confirmed using Phoenix M50 and 16S rDNA PCR. The antibiotic sensitivity to 34 clinically applied antibiotics was determined by Phoenix M50 and the disc diffusion method, according to the protocols of the CLSI and EUCAST. We confirmed the presence of 16 E. coli isolates, of which 87.5% were multi-drug-resistant and 31.25% performed strong biofilms. The possibility for the carrying and transmission of antibiotic-resistance genes to quinolones (qnr), aminoglycosides (aac(3)), β-lactamase-producing plasmid genes ampC, and blaSHV/blaTEM was investigated. We confirmed the carrying of blaSHV/blaTEM in one and ampC in seven isolates. The strains were negative for the virulence genes (ETEC (LT, STa, and F4), EPEC (eae), and STEC/VTEC (stx and stx2all)). The results should contribute to the development of effective measures for limitation and control on the use of antibiotics, which is a key point in the WHO action plan.

Stepwise evolution of carbapenem-resistance, captured in patient samples and evident in global genomics of Klebsiella pneumoniae

The World Health Organization ranks Klebsiella pneumoniae as a priority antimicrobial-resistant (AMR) pathogen requiring urgent study. New strategies for diagnosis and treatment, particularly for those Klebsiella that are classified as carbapenem-resistant Enterobacteriaceae (CRE) need to recognize the increased prevalence of non-carbapenemase producing CRE (non-CP CRE). By integrating diverse Klebsiella genomes with known CRE phenotypes, we successfully identified a synchronized presence of CRE phenotype-related genes in plasmids and chromosomes in comparison to strains with carbapenem susceptible phenotypes. The data revealed a major contribution to CRE comes from the combined effect of chromosome and plasmid genes potentiated by modifications of outer membrane porins. Our computational workflow identified key gene contributors to the non-CP CRE phenotype, including those that lead to an increase of antibiotic expulsion by enhanced efflux pump activity and mobile elements that reduce antibiotic intake, such as IS1 and Tn3-like elements. These findings are consistent with a new model wherein a change to the balance in drug influx and efflux potentiates the ability of some beta-lactamases to enable survival in the presence of carbapenems. Analysis of the large numbers of documented CRE infections, as well as forensic analysis of a case study, showed that this potentiation can occur in short timeframes to deliver a non-CP CRE infection. Our results suggest that the multiple genes that function to build an AMR phenotype can be diagnosed, so that strains that will resist treatment with carbapenem treatment will be evident if a comprehensive genome-based diagnostic for CRE considers all of these sequence-accessible features.

A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription of qnrD. We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode a FAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for an FNR-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.

A Large-Scale Sequencing-Based Survey of Plasmids in Listeria monocytogenes Reveals Global Dissemination of Plasmids

The food-borne pathogen Listeria monocytogenes is known for its capacity to cope with multiple stress conditions occurring in food and food production environments (FPEs). Plasmids can provide benefits to their host strains, and it is known that various Listeria strains contain plasmids. However, the current understanding of plasmid frequency and function in L. monocytogenes strains remains rather limited. To determine the presence of plasmids among L. monocytogenes strains and their potential contribution to stress survival, a comprehensive dataset was established based on 1,921 published genomes from strains representing 14 L. monocytogenes sequence types (STs). Our results show that an average of 54% of all L. monocytogenes strains in the dataset contained a putative plasmid. The presence of plasmids was highly variable between different STs. While some STs, such as ST1, ST2, and ST4, contained few plasmid-bearing strains (<15% of the strains per ST), other STs, such as ST121, ST5, ST8, ST3, and ST204, possessed a higher proportion of plasmid-bearing strains with plasmids found in >71% of the strains within each ST. Overall, the sizes of plasmids analyzed in this study ranged from 4 to 170 kbp with a median plasmid size of 61 kbp. We also identified two novel groups of putative Listeria plasmids based on the amino acid sequences of the plasmid replication protein, RepA. We show that highly conserved plasmids are shared among Listeria strains which have been isolated from around the world over the last few decades. To investigate the potential roles of plasmids, nine genes related to stress-response were selected for an assessment of their abundance and conservation among L. monocytogenes plasmids. The results demonstrated that these plasmid genes exhibited high sequence conservation but that their presence in plasmids was highly variable. Additionally, we identified a novel transposon, Tn7075, predicted to be involved in mercury-resistance. Here, we provide the largest plasmid survey of L. monocytogenes to date with a comprehensive examination of the distribution of plasmids among L. monocytogenes strains. Our results significantly increase our knowledge about the distribution, composition, and conservation of L. monocytogenes plasmids and suggest that plasmids are likely important for the survival of L. monocytogenes in food and FPEs.

Yersinia pseudotuberculosis serotype O:1 infection in a captive Seba’s short tailed-fruit bat (Carollia perspicillata) colony in Switzerland

Background Between February and April 2016, a slight increase in mortality was observed in a colony consisting of 400 captive Seba’s short-tailed bats (Carollia perspicillata). These animals cohabited with other nocturnal animal species in a dome of a private zoo in Switzerland. Results Gross and histological analysis of two (14.3%) out of the 13 animals submitted for necropsy within this period revealed a necrosuppurative pneumonia, hepatitis, splenitis, enterocolitis, and endometritis, with abundant intralesional colonies of Gram-negative rods. Yersinia (Y.) pseudotuberculosis serotype O:1 and biotype 1 belonging to the sequence type ST90 was isolated from the affected organs in both animals. Following this diagnosis, ¼ of the colony (99 animals) was culled and submitted for gross and histopathological analysis, and a bacterial culture selective for Yersinia spp. of lung, liver, and spleen was performed. From these 99 animals, one gravid female was tested and found to be positive for Y. pseudotuberculosis in the absence of clinical symptoms and histopathological lesions. PCR analysis of altogether three bacterial isolates for virulence factors revealed the presence of the ail gene, and one isolate was also positive for the virF and yadA plasmid genes. Conclusions These findings suggest that Carollia perspicillata are susceptible to lethal yersiniosis but do not represent a regular reservoir for Y. pseudotuberculosis. Culling of ¼ of the population was sufficient to limit the spread of this infection among the colony. Moreover, no infections were detected in cohabitant nocturnal animals and caretakers, indicating that the zoonotic risk in this case was low.

Pectobacterium atrosepticum plasmid pPA21A is an important determinant of plant-bacterium pathosystem development

Pectobacterium atrosepticum strain 21A can cause a strong hypersensitive reaction in Nicotiana tabacum. The pPA21A plasmid was found to be responsible for this phenotype. The plasmid genes involved are been identified.