Study Area
The study was conducted in Dar es Salaam, the commercial city of Tanzania, which has a population of 4 364 541 people [3], with highest production and consumption of chicken meat and eggs in Tanzania. The study involved five large poultry slabs in four Districts (Ilala, Ubungo, Temeke and Kinondoni). Approximately 20,000 chicken are slaughtered daily in these five poultry slaughter slabs, which provides about 80% of chicken consumed in Dar es Salaam.
Study Design
This was a cross sectional study conducted between January to June 2020 in four districts, which have largest poultry slabs in Dar es Salaam. The slabs were; Manzese, and Shekilango in Ubungo district, Kisutu in Ilala district, Mtambani in Kinondoni district and Stereo in Temeke district. In this study we targeted broilers and spent layers because they are raised intensively in overcrowded environment, and use of antimicrobials for prophylaxis, growth promotion and in management of infections is very high. Other types of poultry such as indigenous chicken was excluded from the study.
Sampling technique
Using purposive sampling technique, we selected 96 broilers and 96 spent layers, making total of 192 chicken in all the five poultry slabs. Two samples (i.e. cloaca and meat swab) were collected from each chicken, making a total of 384 samples. Cloaca swabs were collected before chicken were slaughtered (at the entry point), while chicken meat swabs were collected after slaughtered (at the poultry slabs).
Specimen collection
Chicken meat and cloaca swabs were collected aseptically using sterile cotton swabs and placed into a sterile tube containing 5 ml of Cary Blair transport medium (Oxoid, Basingstoke, UK). The collected samples were transported in a cool box at 2 to 8 oC containing a thermometer and processed within 2 hours of collection in the Microbiology Teaching Laboratory of the Muhimbili University and Allied Sciences (MUHAS).
Isolation and identification of enterobacteria
In the laboratory, swabs were inoculated onto the MacConkey agar (Oxoid Basingstoke, UK) without antibiotics and incubated aerobically at 37ºc for 24 hours. Identification of E. coli was using colonial morphology, lactose fermentation and Gram stain. Lactose fermenters were subjected to conventional phenotypical identification using a set of biochemical tests including Triple Sugar Iron Agar (TSI), Sulphur indole Motility (SIM) agar and citrate utilization test. Confirmation was done using API 20E identification system for Enterobacteriaceae according to the instructions of the manufacturer (BioMérieux, Marcy-Etoile, France).
Screening and confirmation of ESBL production
Confirmed E. coli were inoculated onto MacConkey agar containing 2 mg/l cefotaxime for preliminary screening of ESBL production. ESBL producers were confirmed using a combination disk method of cefotaxime 30µg alone; combination with clavulanic acid (10 µg) and ceftazidime 30µg alone and combination with clavulanic acid 10 µg. The difference of inhibition zone of more than or equal to 5mm were confirmed as ESBL positive [9]. Klebsiella pneumoniae ATCC 700603 was used as a positive control and E. coli ATCC 25922 as a negative strain.
Antimicrobial susceptibility testing
The antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion method on Mueller Hinton Agar (Oxoid, Basingstoke, UK) based on CLSI 2019 guidelines [9]. Seven antibiotics from different classes were used, which included, ampicillin (10µg), tetracycline (30µg), gentamycin (10µg), ciprofloxacin (5µg), imipenem (10µg), sulfamethoxazole-trimethoprim (1.25/23.5µg), and cefotaxime 30 µg [9].
Colonies of lactose fermenters identified as E. coli were emulsified into sterile saline to achieve turbidity equivalent to 0.5 McFarland standard, which is equivalent to 108 cfu/ml [10]. Suspensions were spread onto Muller Hinton Agar (MHA) using sterile cotton swabs and incubated aerobically at 37 °C for 16 to 18 hours. The inhibition zone of each antimicrobial agent was measured after 16 to 18-hours of incubation and results were interpreted according to the 2018 CLSI guidelines [9]. E. coli strain ATCC 29522 was used as a control strain. A strain was referred to be multidrug resistance (MDR) if it exhibited resistance to at least three different antimicrobial classes [10].
DNA Extraction and Polymerase Chain Reaction (PCR)
ESBL producing E. coli isolates were inoculated on nutrient agar and incubated aerobically at 37 oC for 24 hours. DNA was extracted by boiling in a water bath at 100oC for 10 minutes, followed by centrifugation at 1500 rpm for 3 minutes. The supernatant containing DNA was transferred into sterile Eppendorf PCR tube (Eppendorf AG, Hamburg, Germany) and centrifugation and separation of supernatant were repeated three times. The concentration of DNA was determined by Nano drop spectrophotometer (Biochrom LTD, Cambridge, England) at 260/280 and 260/230 wavelength. DNA were stored at -20oC, before being used for detection of CTX- M and PMQR genes (qnr A, qnr B, qnr S and aac(6')-Ib-cr).
The Dream Tag DNA polymerase kit (Thermo Fisher scientific, US) was used in detection of resistance genes. Total PCR reaction volumes were 25µL, consisting of 10X dream Tag Buffer 5 µL, dNTP 2mM 5 µL, forward and reverse primers were 1 µL each, DNA extract were 2 µL, Dream Tag DNA Polymerase (1.25 U) 1 µL and nuclease free water 10 µL. The primers used in amplification of respective E. coli resistance genes are listed in Table 6.
Molecular detection of CTX -M genes
All ESBL producing E. coli isolates were screened for the CTX-M gene using Uniplex PCR based technique [11]. The process involved initial denaturation at 98 oC for 3 minutes, followed by 35 cycles of denaturation at 98 oC for 15 seconds, annealing at 60 oC for 5 seconds, extension at 72 oC for 45 seconds and final extension at 72 oC for 5 minutes (11).
Detection of PMQR genes (qnr A, qnr B and qnr S)
PMQR resistant genes (qnr A, qnr B and qnr S) were amplified and detected using multiplex PCR assay [12]. The process involved initial denaturation at 94 oC for 5 minutes, followed by 32 cycles of denaturation at 94 oC for 45 seconds, annealing at 53 oC for 1 minute, extension at 72 oC for 1 minute and final extension at 72 oC for 10 minutes (12).
Detection of aac (6')-lb-cr gene.
Aac (6')–lb-cr gene were screened by uniplex PCR based assay [11], using the following the amplification conditions: initial denaturation at 94 oC for 5 minutes, followed by 34 cycles of denaturation at 94 oC for 45 seconds, annealing at 55 oC for 45 seconds, extension at 72 oC for 45 seconds and final extension at 72 oC for 10 minutes [11]. The amplified PCR products were viewed with gel red stain during electrophoresis through 1.5% agarose gel at 100 voltages for 35 minutes.
Data Analysis
The data were entered into Microsoft Excel; proportions were analyzed by Chi-square test. A paired t-test assuming unequal variance was used for comparing overall prevalence and comparing resistance rate among tested antibiotics in SPSS version16 software. A P- value (< 0.05) was considered to be statistically significant.