Average over all C_t values and standard deviation within the analyzed gene subtypes of each beta-lactamase family detected within the 114 control strains.

<p>The runs were performed in two technical replicates and the mean C_t values are indicated.</p><p>n = number of tested genes.</p

Summary of the different beta-lactamase gene combinations occurring among the 20 field isolates.

<p>Summary of the different beta-lactamase gene combinations occurring among the 20 field isolates.</p

Primers and probes used in this study.

<p>Primers and probes used in this study.</p

Detected differences between the previously notified beta-lactamase gene subtype and the real-time results among the 114 used control strains.

<p>Obtained real-time results were confirmed by conventional PCRs and sequencing of the obtained PCR products.</p><p>Additionally detected genes are marked in bolt letters.</p

Identification of Tsetse (<i>Glossina</i> spp.) Using Matrix-Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry

<div><p><i>Glossina (G.)</i> spp. (Diptera: Glossinidae), known as tsetse flies, are vectors of African trypanosomes that cause sleeping sickness in humans and nagana in domestic livestock. Knowledge on tsetse distribution and accurate species identification help identify potential vector intervention sites. Morphological species identification of tsetse is challenging and sometimes not accurate. The matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI TOF MS) technique, already standardised for microbial identification, could become a standard method for tsetse fly diagnostics. Therefore, a unique spectra reference database was created for five lab-reared species of riverine-, savannah- and forest- type tsetse flies and incorporated with the commercial Biotyper 3.0 database. The standard formic acid/acetonitrile extraction of male and female whole insects and their body parts (head, thorax, abdomen, wings and legs) was used to obtain the flies' proteins. The computed composite correlation index and cluster analysis revealed the suitability of any tsetse body part for a rapid taxonomical identification. Phyloproteomic analysis revealed that the peak patterns of <i>G. brevipalpis</i> differed greatly from the other tsetse. This outcome was comparable to previous theories that they might be considered as a sister group to other tsetse spp. Freshly extracted samples were found to be matched at the species level. However, sex differentiation proved to be less reliable. Similarly processed samples of the common house fly <i>Musca dome</i>stica (Diptera: Muscidae; strain: Lei) did not yield any match with the tsetse reference database. The inclusion of additional strains of morphologically defined wild caught flies of known origin and the availability of large-scale mass spectrometry data could facilitate rapid tsetse species identification in the future.</p></div

Laboratory-reared <i>Glossina (G.)</i> spp. selected for the compilation of spectra database.

1<p>Tsetse & Trypanosomiasis Research Institute, Tanga, Tanzania;</p>2<p>International Atomic Energy Agency, Seibersdorf, Austria.</p

Representative spectra of whole insect extraction of male and female <i>Glossina</i> spp.

<p>Mass spectra peak pattern of whole insect extractions of male and female <i>Glossina (G.)</i> spp. The x-axis <i>m/z</i> value stands for mass to charge ratio and the relative intensity of the ions (a.u., arbitrary units) is shown on the y-axis. A) <i>G. morsitans morsitans</i> female, B) <i>G. morsitans morsitans</i> male, C) <i>G. austeni</i> female, D) <i>G. austeni</i> male, E) <i>G. pallidipes</i> female F) <i>G. pallidipes</i> male, G) <i>G. palpalis gambiensis</i> female, H) <i>G. palpalis gambiensis</i> male, I) <i>G. brevipalpis</i> female, and J) <i>G. brevipalpis</i> male.</p

Composite correlation index of tsetse spectra sets.

<p>Evaluation of uniqueness among the spectra sets of 60 tsetse spectra measurements of male (M) and female (F) individuals and their body parts. Composite correlation index matrix was calculated with Biotyper 3.0 software in the mass range of 3000–12000 Da, resolution 4, 4 intervals and auto-correction off. Red indicates relatedness between the spectra sets and dark green indicates incongruence.</p

Representative spectra from the whole insect and different body parts of female <i>Glossina austeni</i>.

<p>Peak pattern of whole and body parts extractions of <i>Glossina austeni</i> female. The x-axis <i>m/z</i> values represent the mass to charge ratio and on the y-axis the relative intensity of the ions (a.u., arbitrary units) is shown. A) Whole insect, B) abdomen, C) head, D) legs, E) thorax and F) wings.</p

Table_2_Transmission pathways of campylobacter spp. at broiler farms and their environment in Brandenburg, Germany.XLSX

Broiler meat is widely known as an important source of foodborne Campylobacter jejuni and Campylobacter coli infections in humans. In this study, we thoroughly investigated transmission pathways that may contribute to possible Campylobacter contamination inside and outside broiler houses. For this purpose we carried out a comprehensive longitudinal sampling approach, using a semi-quantitative cultivation method to identify and quantify transmissions and reservoirs of Campylobacter spp.. Three german broiler farms in Brandenburg and their surrounding areas were intensively sampled, from April 2018 until September 2020. Consecutive fattening cycles and intervening downtimes after cleaning and disinfection were systematically sampled in summer and winter. To display the potential phylogeny of barn and environmental isolates, whole genome sequencing (WGS) and bioinformatic analyses were performed. Results obtained in this study showed very high Campylobacter prevalence in 51/76 pooled feces (67.1%) and 49/76 boot swabs (64.5%). Average counts between 6.4 to 8.36 log10MPN/g were detected in pooled feces. In addition, levels of 4.7 and 4.1 log10MPN/g were detected in boot swabs and litter, respectively. Samples from the barn interior showed mean Campyloacter values in swabs from drinkers 2.6 log10MPN/g, walls 2.0 log10MPN/g, troughs 1.7 log10MPN/g, boards 1.6 log10MPN/g, ventilations 0.9 log10MPN/g and 0.7 log10MPN/g for air samples. However, Campylobacter was detected only in 7/456 (1.5%) of the environmental samples (water bodies, puddles or water-filled wheel tracks; average of 0.6 log10MPN/g). Furthermore, WGS showed recurring Campylobacter genotypes over several consecutive fattening periods, indicating that Campylobacter genotypes persist in the environment during downtime periods. However, after cleaning and disinfection of the barns, we were unable to identify potential sources in the broiler houses. Interestingly, alternating Campylobacter genotypes were observed after each fattening period, also indicating sources of contamination from the wider environment outside the farm. Therefore, the results of this study suggest that a potential risk of Campylobacter transmission may originate from present environmental sources (litter and water reservoirs). However, the sources of Campylobacter transmission may vary depending on the operation and farm environmental conditions.</p