text
string
predicted_class
string
confidence
float16
Screening for putative inhibitors of CsTegu20.6 was performed using GalaxySite , which was employed to predict compounds and binding conformations for CADD. The template search was performed based on experimental structures of template proteins complexed with compounds in the local alignment mode and then was optimized using the conformational space annealing algorithm. Six putative inhibitors were identified: STU, ANP, BK3, CRK, DTQ and MRD (Table S1).
study
100.0
After the two compounds STU and ANP were further screened by predicting the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of all compounds using admetSAR , only STU (staurosporine) was found to be acceptable according to Lipinski’s rule of five (Table S1). The absorption factors for STU resulted in high probabilities (97.3%) for human intestinal absorption, but moderate probabilities for blood brain barrier and CaCo-2 permeability. Under the metabolism profile, STU was found to be a substrate only for cytochrome P450 (CYP450) 3A4, a non-inhibitor for all different forms of CYP450, thus having high CYP inhibitory promiscuity. Under the toxicity profile, STU demonstrated the absence of mutagenic toxicity (a.k.a. AMES toxicity) and carcinogenic effects and also was found to be not toxic for fish and honey bee. Collectively, these data suggest that STU represents a safe and orally-absorbed drug candidate (Figure 7A), whereas the other compounds were ruled out for reasons, such as toxicity for fish (BK3 and CRK), AMES toxicity (DTQ), carcinogenicity (MRD) and violations of Lipinski’s rule (hydrogen bond acceptors, hydrogen bond donors and molecular weight for ANP) (Table S1).
study
100.0
To further investigate the spatial characteristics of the compound binding properties, the protein-compound interaction was analyzed. The associated binding pocket appeared shallow and open in shape. Hydrophobic (Phe9, Thr13 and Tyr27) and electronegative (Asp14 and Glu23) regions were found in the center and wall of the pocket, respectively (Figure 7C,D). One-half of the fused indole and carbazole ring of STU was inserted in the pocket, whereas the rest of the compound was located in the shallow groove. Although no typical hydrogen bonds were identified, STU can tightly bind to CsTegu20.6, resulting in a docking energy of −7.23 kcal/mol (Figure 7B and Table S1). STU, a well-known protein kinase inhibitor, has previously been proposed as an effective drug for protozoan parasites . Its analogues also showed strong inhibitory effects against a number of infectious agents, including antibacterial and immunosuppressive activities . These studies, therefore, provide speculative justification that STU might exhibit the potential to become a leading putative anti-clonorchiasis compound.
study
99.94
Recombinant (r)CsTegu20.6 was purified under native conditions using a histidine tag at the N-terminus. The observed molecular weight was consistent with the predicted molecular mass (Figure 8A). The purified protein was verified using a monoclonal anti-His antibody (Figure 8B). The liquid chromatography-mass spectrometry performed according to our previously reported method identified six specific peptide fragment sequences: 31NNIDPSMIKRWQVLFDADDSGVITLDEFCK60, 41WQVLFDADDSGVITLDEFCK60, 82GPSLPREVDVITATLPLDQQVDIVNEVMR110, 88EVDVITATLPLDQQVDIVNEVMR110, 114NEPFDENLVSK124 and 145GSSWCSFSYEPK156. The peptide sequences matched with those predicted for CsTegu20.6 with a sequence coverage of 56% (Table S2).
study
100.0
PCR experiments showed that an amplicon specific to CsTegu20.6 was detected in the adult worm and metacercariae of C. sinensis, but not in the egg (Figure 9A). A full-length cDNA clone of CsTegu20.6 was used as the positive control. We also confirmed that native CsTegu20.6 was expressed in adult worm and metacercariae using anti-rCsTegu20.6 sera (Figure 9B). As previously described in Figure 5C, CsTegu20.6 was predicted to form homodimers, which can be an unidentified protein complex of molecular weight between the 37-kDa and 50-kDa bands. The lack of expression in the egg possibly arises from the fact that tegumental proteins are differentially expressed in the body according to developmental stages . By the manipulation of its biological aspects, the tegument serves as an important biological means of protection. When encysted metacercariae migrate to the common and hepatic bile ducts in the mammalian host and then grow to adult worms, the juvenile worms are completely exposed to the host immune attack and toxic bile acids during the processes of migration and development . Conversely, similar expression between the adult worm and metacercariae suggests that CsTegu20.6 might be useful as a potential antigen for the early diagnosis of clonorchiasis, which would have the advantage that C. sinensis infections could be detected prior to egg deposition .
study
100.0
As expected, immunolocalization showed that CsTegu20.6 was dominantly distributed at the tegument of the C. sinensis adult worm, using anti-CsTegu20.6 sera as the primary antibody and fluorescein isothiocyanate (FITC)-conjugated anti-rat IgG as the secondary antibody (Figure 10A,B). In contrast, no staining was observed in sections incubated with the pre-immunized serum (Figure 10C,D).
study
100.0
CsTegu20.6 was searched against an expressed sequence tag (EST) database of C. sinensis developmental stages constructed using large-scale sequencing . The nucleotide sequence was translated using the ExPASY Translate tool (http://web.expasy.org/translate/). The ORF was predicted using the ORF-predictor server . The physico-chemical properties of the predicted protein, including molecular weight and pI, were calculated by ProtParam . Functional domains was searched using InterProScan , signal peptides with SignalP 3.0 , protein subcellular localization using TargetP and transmembrane regions with TMHMM . Homologous proteins were collected from a BLASTP search (National Center for Biotechnology Information, Bethesda, MD, USA) . Multiple sequence alignments were generated using MAFFT and were displayed by ESPript .
study
100.0
Although the 3D structure of CsTegu20.6 was modeled using Swiss-Model and I-TASSER , the optimal 3D structure was not constructed because of the unavailability of appropriate templates. Therefore, we used a modified method to obtain the full-length and refined structures of the CsTegu20.6 protein (Figure 1) as follows: (1) the CsTegu20.6 protein sequence was split into D1 and D2 domains based on the disordered region predicted by DisoPred3 (Figure 1A); the C1 fragment was selected as a bridge in order to later combine the two domains; (2) the 3D structures of D1, D2 and C1 were modeled using I-TASSER (Figure 1B); (3) the residue numbers of the D2 domain and the C1 fragment were readjusted to the original numbers in the sequence, renaming them as D2′ and C1′, respectively. Each domain and C1′ fragment was superposed using the TM-Score . Both D1 and D2′ were aligned to the C1′ fragment using the TM-Score so that D1 and D2′ were correctly oriented 5′ to 3′ with respect to each other. Then, the full-length structure was obtained by combining each superposed structure, from which the C1′ fragment was removed manually (Figure 1C); (4) The low free-energy conformations of the combined full-length structure were refined by full-atomic simulations using ModRefiner (Figure 1D). The additional refinement process was performed in two stages. First, the loop regions aa13–20, aa74–88 and aa145–154 were refined by GalaxyLoop using the ‘PS1tbm protocol’ scoring method. Then, both the backbone and side chain of the structure were refined using GalaxyRefine incorporating the “both mild and aggressive relaxation” method.
study
100.0
Structural evaluation and stereochemical quality assessment were performed using several evaluation and validation tools both before and after refinement. The potential errors in the 3D models were evaluated using Ramachandran plots obtained from PROCHECK , ProSA , QMEAN and ERRAT .
other
99.25
Secondary structure elements and the structure topology of CsTegu20.6 were analyzed using ProFunc . The deconSTRUCT and DALI were employed to detect the aligned regions of proteins based on structural similarities. The oligomeric state of the structure was predicted using GalaxyGemini , with subsequent energy minimization. All structure visualization was performed using UCSF Chimera and PyMOL v.099rc6 (http://www.pymol.org).
study
99.9
COACH was used to predict calcium-binding sites in the N-terminal region of CsTegu20.6, based on the identification of analogs with similar binding sites. GalaxySite was employed to predict specifically binding non-metal ligands and their binding conformations for screening putative inhibitors of CsTegu20.6. The detailed information regarding specific protein-compound interactions such as hydrophobic interactions, was visualized using LigPlot+ implemented in GalaxySite. ADMET properties were evaluated using admetSAR . Lipinski’s rule of five and binding energies were calculated using the Molinspiration online server (http://www.molinspiration.com/cgi-bin/properties) and MTiAutoDock , respectively.
study
100.0
The animal care and use protocol was reviewed, and the experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at Korea National Institute of Health (KNIH) (Approval Nos. NIH-06-15, NIH-07-16 and NIH-08-19). The experiments were approved by the Committee on the Ethics of Animal Experiments of the Korean Centers for Disease Control and Prevention (KCDC) (Korean Laboratory Animal Act No. KCDC-122-14-2A). The use of experimental animals was maintained and handled in strict accordance with institutional guidelines at KCDC. The serum samples were collected from experimental rats.
other
99.9
C. sinensis metacercariae were obtained from naturally-infected fish, Pseudorasbora parva, caught in Jin-Ju, South Korea, using previously published methods . We administered 500 metacercariae orally twice to each New Zealand white rabbit (Orient Bio Inc., Seongnam, Korea), and adult worms were collected from the bile ducts of the infected rabbits at 2 months post-infection. Then, the worms were prepared for immunohistochemistry.
study
99.94
The full-length CsTegu20.6 gene sequence was isolated from an EST library of adult worms using polymerase chain reaction (PCR). C1000 TouchTM Thermal Cycler (Bio-Rad Laboratories Inc., Hercules, CA, USA) and TaKaRa LA Taq polymerase (TAKARA, RR042, Shiga, Japan) were used in the PCR reaction. The forward and reverse primers for CsTegu20.6 were 5′-GGG CAA GGT ACC ATG GAG CCA TTC TTA GAA G-3′ and 5′-CCC GTT AAG CTT TCA GCT TGG TGT CTT CCA C-3', incorporating Kpn I and Hind III restriction sites (underlined), respectively. Cycling conditions were as follows: 95 °C for 30 s, followed by 30 cycles of 94 °C for 30 s, 58 °C for 30 s, 72 °C for 60 s and, finally, 72 °C for 10 min. The amplified PCR products were purified, digested with Kpn I and Hind III endonucleases, run on a 1% agarose gel, excised from the gel and ligated into the bacterial expression vector pRSETb (Invitrogen, Carlsbad, CA, USA). After antibiotic selection, positive clones were confirmed by nucleotide sequencing (Macrogen, Seoul, Korea) and transformed into Escherichia coli BL21 (DE3) pLysS (Invitrogen).
study
100.0
Recombinant fusion protein was expressed by isopropyl-β-d-thiogalactopyranoside induction at a final concentration of 0.5 mM at 30 °C for 5 h. Bacterial cells were harvested by centrifugation at 70,000× g for 10 min at 4 °C. The cells were lysed by sonication in buffer (50 mM NaH2PO4, 300 mM NaCl and 10 mM imidazole), and the supernatant was collected after centrifugation at 13,000× g for 30 min. The fusion protein was purified by Ni-NTA affinity chromatography following the manufacturer’s instructions (Qiagen, Gaithersburg, MD, USA). The purified recombinant protein was examined by 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and stained by Coomassie brilliant blue G-250.
study
99.94
The rCstegu20.6 proteins were subjected to 12% SDS-PAGE and subsequently transferred to PVDF membranes (Millipore, 0.45 µm, IPVH00010, Molsheim, France). Non-specific binding was blocked by incubation in blocking buffer (5% skim milk, 20 mM Tris, 500 mM NaCl, 0.05% v/v Tween 20, pH 7.4) at room temperature. The membranes were reacted with HRP conjugated anti-polyhistidine antibody (mouse, polyclonal, Abcam, ab49781, 1:2000 dilution) for 1 h. After washing with TBST, the immunoreactive bands were visualized on the membrane using 4-choloro-1-naphthol solution (Sigma, C6788, St. Louis, MO, USA).
study
99.94
To obtain anti-rCsTegu20.6 sera, Sprague–Dawley rats (Orient Bio Inc., Seongnam, Korea) were used for peptide injection. The initial injection included Freund’s complete adjuvant (Sigma-Aldrich, St. Louis, MO, USA) mixed with purified rCsTegu20.6 (100 µg), and 3 subsequent injections included Freund’s incomplete adjuvant (Sigma-Aldrich) at 1-week intervals. Blood was collected 2 weeks after the final immunization, and its serum was separated as the antisera against CsTegu20.6. The specificity of the antibody was detected by Western blot as described below.
study
100.0
Adult worms, metacercariae and eggs of C. sinensis were homogenized in lysis buffer (40 mM Tris, 7 M urea, 2 M thiourea and 4% CHAPS), respectively. The concentration of each crude extract was determined by the Bradford assay (Bio-Rad Laboratories, Berkeley, CA, USA). A 10-μg sample of each crude extract was subjected to 12% SDS-PAGE and electrotransferred to a polyvinylidene fluoride membrane. The anti-CsTegu20.6 serum (1:1000 dilution) and HRP-conjugated anti-rat IgG (1:2000 dilution) were used primary and secondary antibodies, respectively. Final visualization was performed using the ChemiDocTM imager (Bio-Rad).
study
99.94
Complete ORF transcripts of CsTegu20.6 were amplified from specific stages of C. sinensis, including adult worms, metacercariae and eggs, using the previously described primers. PCR was performed using a thermal cycling profile of 95 °C for 1 min, 30 cycles at 94 °C for 30 s, 55 °C for 30 s and 72 °C for 1 min followed by a 72 °C extension for 10 min. The analysis of transcripts obtained from each cDNA library was performed by 1% agarose gel electrophoresis and ethidium bromide staining.
study
99.94
Immunohistochemistry was performed to investigate the localization of CsTegu20.6 within the adult worm. Fresh-washed adult worms of C. sinensis were fixed with 4% paraformaldehyde, dehydrated by a graded ethanol series and embedded in paraffin blocks. Sections of adult fluke (4 μm thick) were mounted on glass slides, deparaffinized, rehydrated and washed in phosphate-buffered saline (PBS). The slides were incubated with anti-CsTegu20.6 sera diluted 1:100 in PBS at room temperature for 2 h and washed several times in PBS. Non-immunized rat sera were employed as a negative control. The slides were then incubated for 2 h in FITC-conjugated anti-rat IgG (1:200 dilution, Sigma, St. Louis, MO, USA). All specimens were washed and examined using a light/fluorescence microscope (Axioplot, Carl Zeiss, Jena, Germany).
study
99.94
In this study, we identified and characterized CsTegu20.6 using in silico and molecular approaches. A reliable tertiary structure of CsTegu20.6 protein was modelled using combined 3D modeling methods because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. Through the structure-based virtual screening, staurosporine was proposed as a putative inhibitor, which can be used as preliminary data for the development of novel anti-C. sinensis drugs. At the molecular level, CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. CsTegu20.6 localized to the exterior of the tegument in the adult fluke.
study
100.0
Milk has played a major contribution in the human diet in many different countries across the world. Therefore, it is not surprising that considerable attention has been paid over many years to improve milk quality and in particular the hygienic quality. Bacterial contamination in milk can reduce the raw milk quality and create health hazards especially when the milk is contaminated with some certain species of bacteria with their associated enzymes and toxins that may survive pasteurization .
other
99.9
Microbiology to the dairy industry is an important issue, as recent outbreaks of food-borne illness were recorded as a result of consumption of milk and dairy products that had been contaminated with pathogenic organisms or their toxins. As a result, huge attention has been paid on the microbiological analysis of milk and dairy products to evaluate the quality and also to ensure that there are no public health hazards.
other
99.9
Investigations indicated that Escherichia coli O157:H7 is an emerging cause of foodborne illness and that young dairy cattle are a reservoir for it. A particularly dangerous type is referred to as enterohemorrhagic E. coli (EHEC). Infection with EHEC strains often associated with foodborne outbreaks traced to milk, dairy products, and other foods lead to hemorrhagic colitis (bloody diarrhea) and hemolytic uremic syndrome in humans .
other
60.44
Transmission of EHEC to humans occurs by many ways such as through consumption of undercooked meat, vegetables, and water contaminated by feces of carriers, person-to-person and contaminated environment contact. The risk of EHEC infection in humans from dairy farms can occur through the consumption of raw milk, dairy products, and contaminated meat from dairy cattle and through contamination of the dairy environment. Therefore, to reduce the risk of EHEC infection, it is important to improve the measures of control and also to enhance the management and to prevent the transmission of EHEC strains among animals, environment, and humans .
other
99.9
Libya is not an exception where there is a high demand for consumption of both milk and dairy products. It is not unusual that Libyans purchase and consume not only raw cow’s milk but also goat and sheep milk. Traditionally, camel’s milk is consumed raw neither pasteurized nor boiled. Locally made dairy products, such as soft cheeses, fermented milk, and ice cream are manufactured at small-scale dairy parlors, where hygienic measures neither applied nor enforced. Few studies on EHEC O157:H7 have been published from Libya as that linked to diarrhea in children from Libya and dairy cattle in Tripoli .
other
99.7
A total of 108 samples were collected; 44 samples were raw milk (28) Cow, (9) she-camel and (7) goat, and the remaining 64 samples were locally manufactured dairy products: Soft cheeses (10 Ricotta and 21 Massora: Locally made cheese that manufactured by simple method of casein precipitation using food grade diluted organic acids), (5) ice cream and (28) fermented cow’s milk. Samples were randomly collected from different regions of Libya (Janzour, Tripoli, Kremiya, Tajoura, and Tobruk). Collected samples were transferred to the laboratory of Food Hygiene and Control Department, Faculty of Veterinary Medicine, University of Tripoli in an insulated icebox with a minimum of delay to be immediately examined for isolation and identification of existing EHEC.
study
99.94
The collected samples of each product were prepared according to American Public Health Association (APHA). Preparation of samples, decimal dilutions, and culturing techniques for EHEC was performed according to the methods described by the APHA . Briefly, 25 mL/g from each sample was aseptically transferred into a sterile polyethylene stomacher bag and blended with 225 mL of sterile buffered peptone water (Cat. #610098, LIOFILCHEM, Italy) in a stomacher (Stomacher 400, Seaward Medicals, UK) at 230 rpm for 1 min. Serial dilutions were made using sterile 0.1% peptone water.
study
99.94
A volume of 0.1 mL of appropriate dilutions was spread evenly on a dried surface of Tellurite-cefixime-sorbitol MacConkey (TC-SMAC, Oxoid, UK) agar plates . All inoculated plates were incubated at 37±0.5°C for 18-24 h. Typical colonies of E. coli O157 were colorless or neutral/gray with a smoky center and 1-2 mm in diameter. Five typical colonies were picked and cultured on nutrient agar slants and incubated at 35±0.5°C for 18-24 h for further identification by Levine’s eosin-methylene blue (L-EMB, Oxoid, UK) Agar which shows a characteristic green metallic shine colony of EHEC O157:H7.
study
100.0
The procedure of DNA extraction of E. coli O157 isolates was done in the same way as described before . Partial 16S rDNA was amplified using the universal oligonucleotides primers Forward: S-D-Bact-0341-b-S-17 and Reverse: S-D-Bact-0785-a-A-21 adopted from . Universal primers were used as this study was part of a project titled “Genetic authentication of bacterial isolates from meat and milk products in Libya and establishing the Food-borne Libyan-type Bacterial Collection (FLBC).” Therefore, the entire project was not focused on E. coli but also for many other bacterial isolates (total of 330 PCR products were sequenced) from milk and meat products in Libya; hence, the universal primers were used to detect all other bacterial isolates in all samples. The amplified 16S rDNA PCR fragment (464 bp) was excised from the gel, and the DNA was extracted from the gel using GF-1 Ambi Clean kit (Cat. #GF-GC-100, Vivantis, Malaysia). The purified 16S rDNA amplicons were then sequenced in Istituto Zooprofilattico Sperimentale della Lombardia e dell Emilia Romagna, Brescia, Italy, as described before . All sequences will be submitted to the GenBank in the near future once completing of all project studies.
study
100.0
Phylogenetic tree was constructed using neighbor-joining algorithm (http://www.phylogeny.fr/simple_phylogeny.cgi) of partial 16S rDNA nucleotides sequence to show the phylogenetic relationships between local isolates sequences and those between the sequences of E. coli O157: H7 (Sakai and FRIK944 strains), Shigella flexneri, Salmonella Typhi, Proteus vulgaris, and Pseudomonas aeruginosa available in the GenBank, the National Institutes of Health genetic sequence database.
study
99.94
Out of the 108 cultured samples, only 27 (25%) yielded bacterial growth on TC-SMAC suggesting EHEC O157 (Table-1). With the exception of ice cream samples that revealed no growth on TC-SMAC, other samples showed differences in the recovery rate of suspected colonies; the lowest recorded in goat’s milk where only 7.4% (2/27) showed colonies suspected to be EHEC O157, while the highest rates of isolation recorded in Massora cheese 33% (9/27) followed by fermented cow’s milk 26% (7/27) (Table-1). Only 11% (3/27) in each of the raw cow’s milk, raw she camel’s milk and Ricotta samples had growth on TC-SMAC with colonies suspected to be EHEC O157.
study
100.0
Bacterial isolates recovered (27) from growth on TC-SMAC were subjected to molecular analysis by DNA extraction followed by partial sequencing of their 16S rDNA. Results of sequence analysis (Table-2) showed that only 11 isolates (40%) were EHEC (Table-2 and Figure-1). Among those 11 EHEC isolates: 6 (46%) were recovered from fermented cow’s milk, 3 (23%) from raw cow’s milk, while both raw goat’s milk and Maasora gave 2 (15.4%) isolates each (Tables-1 and 2). While none was recovered from the raw camel’s milk, Ricotta and ice cream samples. That would result in an overall isolation rate of 10% (11/108) EHEC O157.
study
100.0
Polymerase chain reaction (PCR) amplification of 16S rDNA (464 bp) of typical bacterial colonies primarily cultivated on tellurite-cefixime-sorbitol MacConkey (TC-SMAC) and purified on Levine’s eosin-methylene blue (L-EMB) agar media. (a) Typical colonies identified as Escherichia coli and agglutinated with anti-O157 latex test. (b) Non E. coli colonies that showed similar morphological characteristic on TC-SMAC and purified L-EMB agar media. Positive and negative controls were included. The PCR products were subjected for electrophoresis in 2% agarose gel incorporated with gel red stain; the identification was based on sequencing of the purified PCR bands and BLAST search.
study
99.94
Citrobacter freundii, Hafnia alvei, Raoultella ornithinolytica, and Enterobacter spp. revealed similar cultural morphology of EHEC on TC-SMAC and L-EMB media, and the correct identification was unraveled by application of 16S rDNA PCR and partial sequencing (Figure-1). The results of the phylogenetic analysis showed that the strains 3301.2, 6412, 6413, 7401, 9405, 6306, 10426 and 3410.2 are closely related among them and with respect to E. coli O157:H7 FRIK944 strain with more than 99% similarity values. Meanwhile, strains 3301.1 and 6308 are related to E. coli O157:H7 Sakai strain (Figure-2 and Table-2).
study
100.0
Phylogenetic tree was constructed using neighbor-joining algorithm of partial 16S rDNA nucleotides sequence showing phylogenetic relationships between the sequences of the local Escherichia coli isolates sequences and E. coli O157:H7 (Sakai and FRIK944 strains) available in databanks.
study
99.94
A markedly large number of people are consuming raw unpasteurized milk and products made from it. Enhanced nutritional qualities, taste, and benefits have all been advocated as reasons for increased interest in raw milk consumption. However, science-based data to substantiate these claims are limited . Food-borne outbreaks due to consumption of dairy products constitute a chronic problem facing food hygienists, as milk and dairy products are subjected to different sources of contamination by many pathogens either from endogenous origin or directly and indirectly from exogenous origin. The origin of contamination by food-borne pathogens varies with the type of product and the mode of production and processing. Treatment and processing of milk inhibit or encourage the multiplication of such organisms as all the nutritional components that make milk and dairy products an important part of the human diet, also support the growth of these pathogenic organisms .
review
99.9
Results obtained in this study showed that EHEC O157 has been isolated and identified from most of the examined milk and dairy products samples except from raw camel’s milk, Ricotta and ice cream samples, as refereeing to positive results confirmed sequencing of by 16S rDNA (Table-1). In our results, the percentage of suspected EHEC growth on TC-SMAC was 25% (27/108), whereas confirmation by sequencing 16S rDNA yielded 10% (11/108). Discrepancies between the isolation rates of bacteria by conventional methods and those by molecular identification (PCR and 16S rDNA sequencing) have been reported earlier .
study
100.0
In this study, the isolation of EHEC from raw milk samples could be attributed to fecal contamination during the milking step . On the other hand, the absence of EHEC in ice cream samples in this study is most likely due to the use of reconstituted milk powder or ready to use ice cream formulas rather than fresh milk.
study
100.0
All the 27 positive milk and products samples tested showed growth of colonies with a metallic green sheen on Levine EMB agar, which was highly suspicious for E. coli. These colonies were cultured on TC-SMAC, the recommended method for the isolation of E. coli O157.
study
99.9
In this study, EHEC O157 was confirmed in 21.4% (6/28) of fermented cow’s milk; this is a high rate of isolation if compared to 9.6% (5/52) which was reported in Nigeria . The existence of EHEC in fermented milk samples could be explained by the acid tolerant property of the organism . Our data revealed that none of the raw she camel’s milk samples were positive for EHEC, however, despite scarcity of information about isolation of EHEC from she camel’s milk, one study from Iran demonstrated that 6.8% (3/44) of she camel’s milk samples collected were positive for EHEC . Our results also showed that 28.6% (2/7) of EHEC isolates were recovered from raw goat’s milk samples; this is to the contrary of another study where the incidence of EHEC O157 in goat’s milk was 0.7% (3/460) in samples collected in Greece , while no E. coli O157 was detected in any of the cheeses made with raw ewe’s and goat’s milk samples from Portugal . Raw cow’s milk yielded 3.5% (1/28) of EHEC O157 positive samples examined in this study. However, the percentage of positive raw cow’s milk samples with EHEC O157 in other studies were 17.4% , 12% , 10% , 2% , and 1.4% .
study
100.0
Besides the risks associated with consuming raw milk, there are concerns over the safety of cheeses made from raw milk. Among soft cheeses only Maasora yielded 9.5% (2/21) of EHEC O157 isolates recovered in this study, this result could be linked to the process of preparing Maasora, since the milk used in this type of cheese is raw without heat treatment. However, the presence of EHEC O157 in locally made fresh soft cheese samples was 6% in a study conducted in Nigeria . There have been food poisoning outbreaks linked to raw milk cheeses, some of these outbreaks were due to pathogenic E. coli . On the other hand, none of the Ricotta samples were positive in this study.
study
100.0
It has been established that consumption of raw milk or its products directly is a high risk and that E. coli O157:H7 can cause severe disease and even death . In the U.S., the Centers for Disease Control and Prevention estimates that EHEC O157:H7 causes approximately 73,000 illnesses, 2000 hospitalizations, and 50-60 deaths each year . In Libya, it is common and widely practiced to manufacture dairy products from raw milk. Isolation of E. coli O157 from milk and dairy products examined in this study could be associated with human diseases following their consumption. However, it is not possible to link our findings with any of the food poisoning cases that were occurred in Libya because of the lack of proper documentation of such cases.
study
99.94
Findings of this study highlighted the need to improve and implement the hygienic practices related to dairy production and to apply the Libyan standards of such products for effective monitoring throughout from production to delivery. Due to the importance of the research, more work on EHEC antibiotic resistance is still ongoing. Moreover, further research is needed to fully study the incidence, prevalence and impact of toxins produced by E. coli and other harmful microorganisms.
study
93.8
AMG, SMA, SKA, AAM, FTG, and IME designed and planned this research work. AMG, EMA, SMA, SKA, HTN, AAM, FTG, and IME were involved in the research by collecting samples and doing the lab work. IB has carried out the sequences of the PCR products in her lab. All authors contributed equally in preparation and revision of the manuscript. All authors read and approved the final manuscript.
other
99.94
In sub-Saharan Africa, supervision of primary healthcare facilities is widely practised as part of service management and ensuring quality of care.1,2,3,4,5 The relationship between the person (or team) providing supervision and the person (or team) receiving it influences its quality. The supervisory relationship has been described as the single most important determinant of supervision outcome, more so than supervision methods.6
other
99.8
A review on supportive forms of supervision in sub-Saharan Africa described its success as relying on the formation of trusting, collaborative supervisory relationships characterised by open, two-way communication.3 In contrast, abusive supervisory relationships discourage supervisees and may harm performance.7,8 It has been suggested that even supportive supervision forms will not be successful, unless there is a good understanding of the human interactions involved.5 Meaningful work relations, including engaging in trusting professional relationships, has been described as a basic human need that determines work motivation.9
review
99.9
Power in the supervisory relationship – here referring to the ability of supervisors to influence a change in providers’ practice – has long been explored in the management sciences.10,11,12,13 The forms of power applied by a supervisor will shape the supervisory relationship. In French and Raven’s classical model, power may be exerted through a mutually accepted right of the supervisor to require certain tasks of a health provider.13 This is legitimised by the supervisor’s professional and hierarchical position.
other
99.9
Other relevant forms of managerial power are reward and punishment.13 These are common within managerial supervision systems in sub-Saharan Africa1,2,4,14 and may be determined through performance evaluations.9 Evaluation has been described as the main manifestation of the supervisory power differential15 and is a known source of tension and anxiety.16,17,18 Studies on supervision in psychotherapy practice found strong yet complicated interactions between the practice of performance evaluation and quality of the supervisory relationship.19 Supervisors carrying dual roles of performance evaluator and clinical supporter may find the trust from supervisees threatened if evaluations take place in the absence of basic mutual understanding.20
review
95.06
Supervisors’ positional power over providers usually implies a special responsibility for promoting effective supervisory relationships.15,19 Inasmuch as the mentioned forms of power do not take account of needs and opinions of providers, they may be described as restrictive,21 which implies a somewhat controlled form of work motivation.9 To the extent they are in accordance with knowledge, interests and needs of the provider, they may be described as promotive,21 indicating rather a self-determined behaviour under autonomous motivation.9
other
99.9
There are around 495 health centres (HCs) in Rwanda, and they deal with more than 90% of all outpatient visits in the health system.22,23 HCs only offer primary healthcare services and have no medical doctors. More than 90% of HC nurses have a basic secondary school–based nursing degree (known as an A2 degree).24
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In Rwanda, a team of external supervisors in each of 39 district hospitals conduct supervision visits to HCs in that district.25 The external supervisors are part of a district health management team. They work within the health management information system and have explicit supervisory functions. A supervisor is usually responsible for supervision within a certain domain such as HIV and TB, laboratory services, maternal and child care, general outpatient clinic services, etc. Depending on the number of HCs under a district hospital, this may in some districts require supervisors to work full time with supervision, including daily field visits sometimes to distant HCs. The size of a supervision team varies according to the number of HCs supervised under the hospital, ranging from as low as 4 to as many as 23 HCs. Anecdotally, supervisors are typically clinically experienced nurses with a higher nursing degree (a so-called A1 or A0 degree) and rarely trained specifically in facilitation of learning or interpersonal communication.
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External supervision of HCs includes two categories of supervision visits, in practice often combined, conducted by the same team of supervisors: (1) evaluative and (2) formative.14 Evaluative supervision predominates, not least because of a monthly frequency for some tasks. It involves performance marking of indicators of specific services (not of individual providers) to determine reward size to HCs in performance-based financing (PBF). This may be distributed as salary bonuses among providers, as determined by the HC manager.14,26 Formative or technical supervision visits are expected yet unelaborated in official documents on health system strategy and monitoring.27,28 It emerges as a distinct, intended practice aiming to build staff capacity in various services, but problematised by providers and supervisors as missing or insufficient.14
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Supervisors are not paired with individual providers and often meet new supervisory counterparts as providers may shift tasks.29 Whatever the supervision frequency and familiarity between actors, external supervision of HCs unfolds in essence as a complex interaction between supervisors and providers, whose relationship has not been thoroughly studied in Rwanda, and rarely on the African continent.
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This study aimed to explore key characteristics of the relationship between healthcare providers in Rwandan HCs and their external supervisors from the district hospital, with particular focus on exploring major challenges for building effective supervisory relationships and potential avenues to address these. The paper represents the second of two papers using the same overall set of data, where the first paper14 focused on the relationship between evaluative and formative supervision functions.
study
89.4
This is a qualitative study. While we do not claim allegiance with a particular qualitative research tradition, this study was inspired by principles from grounded theory, particularly by using data to propose a theoretical model for improving the supervisory relationship.
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90.3
We purposefully considered the number of HCs in a district for our sampling because this may influence the number of external supervisors in a team and how much time the supervision team spends on field visits to HCs, which we assumed could impact the supervision experience among supervisors and providers. We therefore included a supervision team from a district with a high number of HCs, a team with few HCs and a team from a district with an average number of HCs. To optimise the chance of retrieving precise recollections, we asked providers from the HC most recently supervised in each of these three districts to participate in a provider discussion. For the same reason, we excluded providers who had not experienced supervision in the past 6 months. HC managers were excluded from the provider FGDs with the intention to set a discussion among peers and reduce social desirability bias. FGDs took place in undisturbed rooms at participants’ main work facility, and participants were offered a drink.
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To further deepen the discussion of solutions to challenges in the supervisory relationship, two supervisors and three providers who participated constructively in a FGD also took part in a mixed seventh FGD (see Data collection methods). This was held in a private room at a restaurant.
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We observed a humorous atmosphere when engaging with providers or supervisors in separate groups, and none so on encounters bringing them together. This indicated warm collegial bonds within rather than between these professional groups. This was one reason to use FGDs within groups of peer colleagues to explore the potentially sensitive issue of how one group of professionals relates to another. Further reasons are provided elsewhere.14
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All FGDs were conducted with minimal moderator involvement to minimise participants’ attention on the moderator and maximise participants’ attention towards each other.14,30,31,32 Thus, participants were facing each other, and the moderator was seated in the background mostly remaining passive and silent, only contributing to steer a discussion back to the topic at hand, clarify topics, probe a relevant discussion if needed or suggest an opinion from relatively silent participants. The moderator was a local social scientist (SI) with experience in conducting group discussions. We presented participants with eight discussion topics directly or indirectly related to the supervisory relationship: (1) Supervision experiences in general, (2) Aims of supervision, (3) Positive experiences, (4) Negative experiences, (5) Supervisors’/supervisees’ (the other’s) behaviour, (6) Supervisors’/supervisees’ (the other’s) view of supervisees/supervisors, (7) Training vs inspection and (8) Recommendations. Some of these (topics 1, 3, 4, and 8) were directly relevant both to this study and the related study,14 some mainly to this study (topics 5 and 6) and some (topics 2 and 7) mainly to the related study.14
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100.0
Participants in the mixed FGD were presented with excerpts from previous FGDs about challenges in the supervisory relationship and asked to discuss these. The aim was to gain further nuances and to challenge robustness of the findings of those FGDs, and to retrieve a balanced, two-sided discussion on potential approaches to challenges in the supervisory relationship.
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We applied the framework approach for data analysis.33 Four coders familiarised themselves with the transcripts and open-coded them paragraph by paragraph. Over multiple meetings, coders discussed and agreed on major code categories for each FGD separately, and subsequently harmonised these to attain one final thematic index covering all FGDs. Two researchers used this to index the material, and intercoder agreement was compared paragraph by paragraph to produce a single harmonised coding of transcripts. One researcher read charted compilations of the indexed material as well as the full material several times, and over discussions among co-authors seven main themes suitable for presentation of findings pertaining to the study aim were determined among several in the thematic index. The software MAXQDA11.2 was used for this process including charting the content of emerging themes.14,33,34
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To test transferability, our findings were presented at three different meetings (latest in October 2016) to a total of 8 providers and 13 supervisors (among whom 4 had participated in FGDs) for critique and discussion to further refine analysis and conclusions. This did not lead to any significant changes and is considered an important contribution to trustworthiness of the findings.
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This study was approved by the Faculty of Medicine Research Ethics Committee at the National University of Rwanda (Review Approval Notice N0 15/FoMREC/2013). Signed informed consent was obtained from all study participants prior to participation. The mixed FGD put together three providers and two supervisors from separate districts to avoid influencing or harming existing supervisory relationships.
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As the table shows, among the 16 participating providers 12 were female, 13 above 30 years and all had worked more than 4 years as a nurse. Ten had only the lowest A2 nursing degree taken as part of secondary school, while five had an A1 full nursing degree and one the advanced A0 bachelor degree. Among the 15 supervisors, 11 were male, 14 above 30 years and experience as a supervisor ranged from 1 to 10 years.
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Concerning participants’ contributions, providers contributed 43% of the total number of characters in the transcripts and supervisors 57%. Individual contributions varied from accounting for a minimum of 1% to a maximum of 7% of all characters, with an average of 3% per provider and 4% per supervisor.
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We describe our findings under seven main themes pertaining to the supervisory relationship that emerged from inductive analysis: Power relation; provider competence; emotions in supervision; communication problems; trust in supervisors; coping and reacting; and building the relationship. The term ‘s/he’ and ‘him/her’ within quotes represents a translation of the genderless subject found in the Kinyarwanda language.
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The power relation between supervisors and providers was discussed in all FGDs. An essential form of power available to supervisors is related to PBF rewards, which require regular performance marking aimed to regulate the behaviour of providers. Its flip side is a sense of punishment or conflict when marks are low or rewards lack, as indicated by a supervisor in FGD3: ‘When it comes to the sense of evaluation, conflicts arise. It is a conflict of interest because it involves marks between brackets. It becomes a punishment.’ (S15, male, A0 degree)
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Disciplinary action against providers was another power source in the potential form of punishment, and something supervisors in general found important. Some felt it was problematic that this power decreased in recent years. For instance, supervisors no longer had the power to suggest or carry through a firing of individual HC staff.
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Providers shared stories of supervisors’ inappropriate use of power or active display of a superior hierarchical position. In FGD4, this was often referred to as a ‘superiority complex’: ‘They [supervisors] always want to show they are on the above position, treading on you. Therefore, you feel you have to tremble and be afraid.’ (P4, female, A2 degree)‘That’s the way they normally behave. They often have a superiority complex [All agreeing].’ (P1, female, A2 degree)
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Sometimes supervisors were likened to police or to businessmen who would treat providers like domestic workers. Supervisors themselves acknowledged that an inappropriate use of power could take place in which supervisors imposed their views, and providers might not get a proper opportunity to talk. Some supervisors showed understanding for the feeling of inferiority among providers by comparing with their own experiences of being supervised.
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There were no attempts to justify an inappropriately authoritative behaviour among supervisors. Some providers saw it as a sign of supervisor insecurity, as this dialogue in FGD6: ‘You may also have [show] all s/he is asking you and get low marks because s/he wants to keep confidence for it is not her/his domain.’ (P13, female, A2 degree)‘Therefore, if those who come are not in your domain nor have a more advanced level … they try to complicate things … to show you that they know more than you.’ (P14, female, A2 degree)
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Here, we present perceptions concerning the competence of primary healthcare providers, as most other headings relate to the competence and behaviours of supervisors. Supervisors generally commended the work of providers and acknowledged their stressful working conditions, including shortage of staff. At the same time, some supervisors spoke in generalising or derogatory terms about HC nurses’ competence level, such as a supervisor in FGD1: ‘We can call these employees [HC staff] “second hand employees” or “second category employees”, because those who are in the first category are able to come and work at the hospital.’ (S2, male, A0 degree)
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Several supervisors described providers in terms essentially separating them in to those with high and low performance, as in FGD1: ‘Those who show interest [in supervision] as he said, are those who generally try to do everything as well as they can. Those other ones who need to be reminded are those ones who generally don’t produce quality work.’ (S4, female, A1 degree)
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All supervisor discussions described providers who failed to implement changes as recommended or appeared uninterested in supervision. This was often perceived as a behavioural problem, sometimes termed resistance to change. Some supervisors showed frustrations with encountering such resistance. Multiple paragraphs indicated the dilemma that providers with performance difficulties could attempt to dodge supervision, such as a supervisor in FGD1: ‘Those [providers] who are disorganized are the ones who avoid anybody who would train them on how they should do their work.’ (S4, female, A1 degree)
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Supervisors did not give clear explanations for resistance or avoidance among providers. Many supervisors would involve HC managers when providers had problems to perform well. Another approach was to carefully reflect on how to help, as expressed by a supervisor in FGD2: ‘When s/he who has some weaknesses doesn’t want to move from one point to another … we should look for a strategy to help them.’ (S6, male, A0 degree)
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Some providers would acknowledge the problem of failure to change their practice, and some related it to a lack of self-or peer supervision. A humble and supportive attitude of the supervisor appeared particularly important when dealing with providers who have performance difficulties. This indicated that resistance to change may reflect an unfit support, which may determine the outcome of supervision, as this nurse in FGD5 expressed: ‘Sometimes the supervisor comes in a good mood, talking to you friendly. … And even if there may be a mistake, s/he corrects you calmly. … Next time, s/he finds that you have adjusted it because s/he had come humbly and with good temper.’ (P8, female, A2 degree)
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‘Sometimes the supervisor comes in a good mood, talking to you friendly. … And even if there may be a mistake, s/he corrects you calmly. … Next time, s/he finds that you have adjusted it because s/he had come humbly and with good temper.’ (P8, female, A2 degree)
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Emotions shape and are triggered by interpersonal relationships. Although discussion topics did not specifically ask about emotions, thematic codings of emotions (including fear, shame, embarrassment, humility, anger, frustration, etc.) were among the most utilised. Fear emerged as the most frequently described emotion, in all cases supervisees’ fear of supervision/supervisors. Several providers described their fear with classical symptoms of anxiety or even panic, such as excessive sweating, sudden urge to go to the toilet or palpitations upon seeing the supervisors or their car. It was indicated that the supervisor–provider relationship is one between individuals, and fear was sometimes related to an individual supervisor.
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Supervisors found that dealing with supervisees’ fear of supervision was a natural part of their work. They could relate to this fear by thinking about their own experiences of being supervised, as in FGD2: ‘It doesn’t happen at health centres only. Even if he [a national supervisor] comes to give us some advice, we first feel discomfort. … That fear is in the human nature [other participants repeat agreeingly].’ (S8, male, A1 degree)
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Supervisors and providers generally related the fear to evaluations and performance marks. A supervisor in FGD2 said: ‘You arrive there and they feel as if the universe has fallen on them [afraid and worried] … they feel like you are always going to give them marks.’ (S7, male, degree not reported)
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Both supervisors and providers questioned the capacity to learn under fear and mentioned that fear can harm performance, as a provider in FGD6: ‘You can never feel secure when you are under supervision. By just learning that it is coming, you … you can even drop down what you have because of fear, [laughs]. … You lose marks! Why? Because of fear.’ (P14, female, A2 degree)
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A provider in FGD6 expressed that one could start forgetting because of fear: ‘When you hear that they [supervisors] have come, you can even lose your mind and forget where you have put the filing cabinet. … You do not feel they are coming to help you but rather you feel anxious.’ (P16, female, A0 degree)
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Other emotions directly or indirectly related to supervision were anger and rage, and some described situations where providers and supervisors had been in harsh confrontations, almost fights. Also, supervisors found that providers often felt embarrassed during their interaction. A supervisor in FGD1 thought that especially providers with performance difficulties felt ashamed: ‘Those who have a low level of knowledge … feel ashamed. … Maybe s/he thinks: “Perhaps s/he [supervisor] has discovered that I am stupid or that I have little competency and then s/he has come for challenging me and reporting me to my superiors”.’ (S2, male, A0 degree)
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‘Those who have a low level of knowledge … feel ashamed. … Maybe s/he thinks: “Perhaps s/he [supervisor] has discovered that I am stupid or that I have little competency and then s/he has come for challenging me and reporting me to my superiors”.’ (S2, male, A0 degree)
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Supervisors and providers consistently described supervisors’ communication style as essential for the supervisory relationship. A provider in FGD4 described how rude interpersonal communication made her feel: ‘S/he [supervisor] added: “Anyway, on the asphalt road [health center is near an asphalt road], you are all the same like this.” … My God, I felt sad.’ (P4, female, A2 degree)
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Providers expressed that the damage of a derogatory or rude communication style was not easily mended even if supervisors provided good advice. Rude communication may leave permanent negative memories, as a provider described in the mixed FGD: ‘It was my first time to work in that service and they came to supervise. … S/he told my boss “why have you appointed that ignorant [person] there?”. That thing has never got out of my mind until this hour.’ (P3, female, A1 degree)
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Rude communication was especially linked to the discussion of mistakes, as this provider in FGD5 explained: ‘Maybe s/he [supervisor] finds out that the same mistake s/he had seen you with last time still exists. Instead of looking for how to adjust it together, it becomes the reason to say that you do nothing in the department, … you are useless there.’ (P7, female, A2 degree)
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‘Maybe s/he [supervisor] finds out that the same mistake s/he had seen you with last time still exists. Instead of looking for how to adjust it together, it becomes the reason to say that you do nothing in the department, … you are useless there.’ (P7, female, A2 degree)
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In FGD3, a supervisor suggested performance evaluations make communication prone to conflicts: ‘Staff of health centres views us as people who have come to create conflicts … because when s/he gets few marks in evaluation, s/he says “it’s going to affect me in PBF. … Now I am not going to get on well with my boss”.’ (S14, male, degree not reported)
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Issues related to supervisees’ trust in supervisors were mentioned in all FGDs, and trust was found essential for successful supervision including disclosure of weaknesses, as indicated by a supervisor in FGD3: ‘Supervision should be done in such a way that s/he [provider] can show you where s/he has weaknesses and even orienting you saying “I have a weakness here, what can you do to help me?” However, instead of doing that, s/he hides something from you.’ (S14, male, degree not reported)
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‘Supervision should be done in such a way that s/he [provider] can show you where s/he has weaknesses and even orienting you saying “I have a weakness here, what can you do to help me?” However, instead of doing that, s/he hides something from you.’ (S14, male, degree not reported)
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Providers accepted that supervisors had to report to HC managers when attitudes or competences were considered inappropriate. However, several providers complained this was done in improper ways which could harm the trust, such as a provider in FGD4: ‘There were some things which were not well completed. Then, s/he [supervisor] thereafter told the chief [HC manager] … “What does s/he do in that service?” Yet, I had been working in that service for two years, and s/he talked to my employer without telling me anything. That shows s/he held me up to ridicule without even coming for training me.’ (P3, female, A1 degree)
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‘There were some things which were not well completed. Then, s/he [supervisor] thereafter told the chief [HC manager] … “What does s/he do in that service?” Yet, I had been working in that service for two years, and s/he talked to my employer without telling me anything. That shows s/he held me up to ridicule without even coming for training me.’ (P3, female, A1 degree)
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In FGD4, another provider told a story about public embarrassment: ‘If s/he [supervisor] talks about you publicly, … you directly become discouraged up to the point that you feel you would hide yourself under this table…. Imagine 13 health centres [at a coordination meeting] with 3 persons per health center, and s/he [supervisor] makes you stand up…. Something you were discussing as two people, s/he directly raises the point among all the participants.’ (P2, female, A1 degree)
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‘If s/he [supervisor] talks about you publicly, … you directly become discouraged up to the point that you feel you would hide yourself under this table…. Imagine 13 health centres [at a coordination meeting] with 3 persons per health center, and s/he [supervisor] makes you stand up…. Something you were discussing as two people, s/he directly raises the point among all the participants.’ (P2, female, A1 degree)
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A number of coping methods and reactions were demonstrated in response to the challenges above. Some providers felt unable to speak during supervision and simply remained silent. Avoidance of supervision, as mentioned, appeared common, here described in a dialogue of two supervisors in FGD1: ‘They [providers] usually tend to hide themselves. Upon sight of the car and upon recognition of people who come in it, each one tries to hide him/herself.’ (S4, female, A1 degree)‘Few are those who are happy about it [supervision]. … They are sort of disturbed, … afraid of something which makes some of them tend to go and hide. We see it, we really agree on that fact that some of them go and hide themselves.’ (S1, male, A0 degree)
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Several providers showed a sense of apathy when describing a negative supervision experience. A provider in FGD4 showed a somewhat fatalistic attitude when explaining how reproachful words may ignite conflict: ‘Supervisors themselves come and tell us like “It’s known you at [Name of HC] have become impossible to manage”. You cannot quarrel with him/her; you only say [think] “That’s ok, take it as you already have it in your mind”. You do not tell them anything with humiliation/humility until God will give the final answer.’ (P4, female, A2 degree)
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‘Supervisors themselves come and tell us like “It’s known you at [Name of HC] have become impossible to manage”. You cannot quarrel with him/her; you only say [think] “That’s ok, take it as you already have it in your mind”. You do not tell them anything with humiliation/humility until God will give the final answer.’ (P4, female, A2 degree)
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Supervisors noticed the apathy as well, and saw HC managers as an influential actor, as in FGD1: ‘There are also those who don’t mind anything. It is as if they could say to supervisors “Do your job quickly and let us do our usual businesses”. … This happens mostly to people who are unhappy about their leadership or leaders, they are the ones who think that supervisors just come to disturb them or make them waste their time.’ (S2, male, A0 degree)
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