Surveillance study on pathogenic Acinetobacter species in freshwater environment of the Amathole and Chris Hani District Municipalities, Eastern Cape, South Africa
- Authors: Adewoyin, Mary Ayobami
- Date: 2019-09
- Subjects: Acinetobacter infections , Acinetobacter , Nosocomial infections
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19836 , vital:43257
- Description: This study evaluates the occurrence of medically relevant Acinetobacter species in three rivers, namely; Keiskamma, Tyhume and Great Fish in the Eastern Cape Province, South Africa in one year sampling regime (April 2017 - March 2018). The physicochemical parameters (pH, temperature (TEM), electrical conductivity (EC), total dissolved solids (TDS), salinity (SAL), total suspended solids (TSS), turbidity (TBS), dissolved oxygen (DO) and biological oxygen demand (BOD)) of the water bodies were measured. The presumptive Acinetobacter species recovered from the freshwater resources were recorded and further confirmed using molecular techniques. Similarly, confirmed isolates were subjected to speciation using species-specific primer sets for A. baumannii and A. nosocomialis. Also, virulence genes namely; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were also determined using molecular method. In addition, the antibiogram characteristics of A. baumannii and A. nosocomialis isolated from the water samples were determined using standard methods. The antibiotic susceptibility test was performed using a panel of 12 antibiotics belonging to the aminoglycosides (amikacin, AK and gentamicin, GM), β-lactam/β-lactamase-inhibitor combinations (piperacillin-tazobactam, PTZ), cephems (ceftazidime, CAZ, cefotaxime, CTX, and cefepime, CPM), carbapenems (imipenem, IMI and meropenem, MEM), fluoroquinolones (ciprofloxacin, CIP), folate pathway inhibitors (Trimethoprim/sulfamethoxazole, TS), lipopeptides (Polymyxin B, PB) and tetracyclines (tetracycline, TET). Similarly, antibiotic resistance genes (ARGs) present in the Acinetobacter isolates were investigated including aminoglycoside resistance genes (aacC2, aphA1 and aphA2), β-lactamases resistance genes (blaTEM, blaSHV, blaOXA-1-like, blaCTX-M(GROUP 1), blaCTX-M(GROUP 2), blaCTX-M(GROUP 9), blaVEB, blaGES, blaPER, blaCTX-M-8/-25, blaOXA-48-like, blaVIM, blaIMP and blaKPC), fluoroquinolones resistance genes (qnrA, qnrB, qnrC, qnrD and qnrS), sulfonamide resistance genes (sul1 and sul2), and tetracycline resistance genes (tetA, tetB, tetC, tetM, tetL and tetO). The pH, EC, TDS, SAL, TEMP, TSS, TBS, DO, and BOD for Tyhume River ranged as follows: 7.2-7.7, 125-141 μS/cm, 62-71mg/L, 0.06- 0.07 PSU, 11.3-20.2oC, 30.0-89.6 mg/L, 35.0-96.0 NTU, 8.2-9.8 mg/L, 2.0-4.2 mg/L, while for Great Fish River, the parameters were 8.0-8.2, 274-369 μS/cm, 137-184mg/L, 0.13-0.18PSU, 12.7-22.3oC, 44.3-99.4 mg/L, 48.0-214.0 NTU, 7.8-9.9 mg/L, 3.1- 4.9 mg/L, and at Keiskamma River they were 7.5-7.9, 153.2-285.0 μS/cm, 86-143 mg/L, 0.07-0.14 PSU, 11.0-21.4oC, 27.0- 55.6 mg/L, 31-61 NTU, 8.3-9.8 mg/L, 3.0-6.0 mg/L. A total of 1107 presumptive Acinetobacter spp. were recovered from the rivers sampled of which 428, 370 and 309 isolates were recovered from Tyhume, Great Fish and Keiskamma rivers respectively. However, only 844 was confirmed positive for the genus Acinetobacter and are recovered in the proportions 285 (77 percent), 219 (70.9 percent) and 340 (79 percent) from Great Fish, Keiskemma and Tyhume rivers respectively. Our finding revealed that 410 (48.58 percent) and 23 (2.7 percent) of the isolates were confirmed to be A. baumannii and A. nosocomalis respectively. Also, 308 (75.12 percent percent) A. baumannii and 3 (13.04 percent) A. nosocomialis isolates exhibited one or more virulence genes out of the seven tested, whereas 102 (24.88 percent) and 20 (86.95 percent) of the A. baumannii and A. nosocomialis isolates did not harbour any virulence gene. Additionally, OmpA was the most prevalent (p<0.05) virulence gene found in A. baumannii with 69 (45.10 percent), 52 (50.98 percent) and 77 (49.68 percent) isolates from Great Fish, Keiskamma and Tyhume rivers respectively. The rates of susceptibilities of A. baumannii and A. nosocomialis to the antibiotics followed the order; Piperacillin-tazobactam (72.8 percent ; 73.9 percent), Ceftazidime (70.5 percent ; 91.3 percent), Cefotaxime (16.8 percent ; 17.4 percent), Cefepime (88.5 percent ; 95.7 percent), Imipenem (95.9 percent ; 100 percent ), Meropenem (92.7 percent ; 91.3 percent), Amikacin (97.6 percent ; 91.3 percent), Gentamicin (89.8 percent ; 87 percent), Polymyxin B (84.4 percent ; 91.3 percent), Tetracycline (74.7 percent ; 78.3 percent), Ciprofloxacin (75.9 percent ; 78.3 percent) and Trimethoprim/sulfamethoxazole (74.0 percent ; 73.9 percent) respectively. Both A. baumannii and A. nosocomialis were highly susceptible to all the antimicrobials tested except cefotaxime where 64 percent and 78 percent intermediate responses were observed in the species. At least 10 isolates of A. baumannii were resistant against each of the antibiotics used. The modal multiple antibiotics resistance phenotypes (MARPs) for Acinetobacter spp. was MARP 3 (29.87 percent) and the least was MARP 10 and 11 (2.6 percent each). The antimicrobial resistance index (ARI) was higher at two sampling sites KE2 (0.33) and TY1 (0.22). Similarly, MARI showed that sampling sites KE2 was a hotspot for multidrug-resistant Acinetobacter spp. Of the five classes of ARGs studied, there was a widespread of β-lactamases (blaTEM) in the two Acinetobacter species, followed by sul2, which were detected in 67 (63.2 percent) and 44 (49.4 percent) isolates respectively, across the rivers studied. We conclude that aquatic resources of the study community are important reservoirs of pathogenic Acinetobacter species and antibiotic resistance determinants. The occurrence of clinically-important Acinetobacter species suggests possible contamination of these selected rivers which are consumed by humans and livestock, as well as being used for irrigation system, and this constitutes a risk to public health. It also shows that A. baumannii and A. nosocomialis can thrive in the aquatic environment. This study suggests that direct utilization of water from these sources for domestic and other purposes without any form of pre-treatment should be avoided. It is, therefore, necessary for regulatory authorities to monitor the release of domestic and industrial wastewater into these water bodies in order to prevent outbreaks of epidemics. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2019
- Full Text:
- Date Issued: 2019-09
- Authors: Adewoyin, Mary Ayobami
- Date: 2019-09
- Subjects: Acinetobacter infections , Acinetobacter , Nosocomial infections
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19836 , vital:43257
- Description: This study evaluates the occurrence of medically relevant Acinetobacter species in three rivers, namely; Keiskamma, Tyhume and Great Fish in the Eastern Cape Province, South Africa in one year sampling regime (April 2017 - March 2018). The physicochemical parameters (pH, temperature (TEM), electrical conductivity (EC), total dissolved solids (TDS), salinity (SAL), total suspended solids (TSS), turbidity (TBS), dissolved oxygen (DO) and biological oxygen demand (BOD)) of the water bodies were measured. The presumptive Acinetobacter species recovered from the freshwater resources were recorded and further confirmed using molecular techniques. Similarly, confirmed isolates were subjected to speciation using species-specific primer sets for A. baumannii and A. nosocomialis. Also, virulence genes namely; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were also determined using molecular method. In addition, the antibiogram characteristics of A. baumannii and A. nosocomialis isolated from the water samples were determined using standard methods. The antibiotic susceptibility test was performed using a panel of 12 antibiotics belonging to the aminoglycosides (amikacin, AK and gentamicin, GM), β-lactam/β-lactamase-inhibitor combinations (piperacillin-tazobactam, PTZ), cephems (ceftazidime, CAZ, cefotaxime, CTX, and cefepime, CPM), carbapenems (imipenem, IMI and meropenem, MEM), fluoroquinolones (ciprofloxacin, CIP), folate pathway inhibitors (Trimethoprim/sulfamethoxazole, TS), lipopeptides (Polymyxin B, PB) and tetracyclines (tetracycline, TET). Similarly, antibiotic resistance genes (ARGs) present in the Acinetobacter isolates were investigated including aminoglycoside resistance genes (aacC2, aphA1 and aphA2), β-lactamases resistance genes (blaTEM, blaSHV, blaOXA-1-like, blaCTX-M(GROUP 1), blaCTX-M(GROUP 2), blaCTX-M(GROUP 9), blaVEB, blaGES, blaPER, blaCTX-M-8/-25, blaOXA-48-like, blaVIM, blaIMP and blaKPC), fluoroquinolones resistance genes (qnrA, qnrB, qnrC, qnrD and qnrS), sulfonamide resistance genes (sul1 and sul2), and tetracycline resistance genes (tetA, tetB, tetC, tetM, tetL and tetO). The pH, EC, TDS, SAL, TEMP, TSS, TBS, DO, and BOD for Tyhume River ranged as follows: 7.2-7.7, 125-141 μS/cm, 62-71mg/L, 0.06- 0.07 PSU, 11.3-20.2oC, 30.0-89.6 mg/L, 35.0-96.0 NTU, 8.2-9.8 mg/L, 2.0-4.2 mg/L, while for Great Fish River, the parameters were 8.0-8.2, 274-369 μS/cm, 137-184mg/L, 0.13-0.18PSU, 12.7-22.3oC, 44.3-99.4 mg/L, 48.0-214.0 NTU, 7.8-9.9 mg/L, 3.1- 4.9 mg/L, and at Keiskamma River they were 7.5-7.9, 153.2-285.0 μS/cm, 86-143 mg/L, 0.07-0.14 PSU, 11.0-21.4oC, 27.0- 55.6 mg/L, 31-61 NTU, 8.3-9.8 mg/L, 3.0-6.0 mg/L. A total of 1107 presumptive Acinetobacter spp. were recovered from the rivers sampled of which 428, 370 and 309 isolates were recovered from Tyhume, Great Fish and Keiskamma rivers respectively. However, only 844 was confirmed positive for the genus Acinetobacter and are recovered in the proportions 285 (77 percent), 219 (70.9 percent) and 340 (79 percent) from Great Fish, Keiskemma and Tyhume rivers respectively. Our finding revealed that 410 (48.58 percent) and 23 (2.7 percent) of the isolates were confirmed to be A. baumannii and A. nosocomalis respectively. Also, 308 (75.12 percent percent) A. baumannii and 3 (13.04 percent) A. nosocomialis isolates exhibited one or more virulence genes out of the seven tested, whereas 102 (24.88 percent) and 20 (86.95 percent) of the A. baumannii and A. nosocomialis isolates did not harbour any virulence gene. Additionally, OmpA was the most prevalent (p<0.05) virulence gene found in A. baumannii with 69 (45.10 percent), 52 (50.98 percent) and 77 (49.68 percent) isolates from Great Fish, Keiskamma and Tyhume rivers respectively. The rates of susceptibilities of A. baumannii and A. nosocomialis to the antibiotics followed the order; Piperacillin-tazobactam (72.8 percent ; 73.9 percent), Ceftazidime (70.5 percent ; 91.3 percent), Cefotaxime (16.8 percent ; 17.4 percent), Cefepime (88.5 percent ; 95.7 percent), Imipenem (95.9 percent ; 100 percent ), Meropenem (92.7 percent ; 91.3 percent), Amikacin (97.6 percent ; 91.3 percent), Gentamicin (89.8 percent ; 87 percent), Polymyxin B (84.4 percent ; 91.3 percent), Tetracycline (74.7 percent ; 78.3 percent), Ciprofloxacin (75.9 percent ; 78.3 percent) and Trimethoprim/sulfamethoxazole (74.0 percent ; 73.9 percent) respectively. Both A. baumannii and A. nosocomialis were highly susceptible to all the antimicrobials tested except cefotaxime where 64 percent and 78 percent intermediate responses were observed in the species. At least 10 isolates of A. baumannii were resistant against each of the antibiotics used. The modal multiple antibiotics resistance phenotypes (MARPs) for Acinetobacter spp. was MARP 3 (29.87 percent) and the least was MARP 10 and 11 (2.6 percent each). The antimicrobial resistance index (ARI) was higher at two sampling sites KE2 (0.33) and TY1 (0.22). Similarly, MARI showed that sampling sites KE2 was a hotspot for multidrug-resistant Acinetobacter spp. Of the five classes of ARGs studied, there was a widespread of β-lactamases (blaTEM) in the two Acinetobacter species, followed by sul2, which were detected in 67 (63.2 percent) and 44 (49.4 percent) isolates respectively, across the rivers studied. We conclude that aquatic resources of the study community are important reservoirs of pathogenic Acinetobacter species and antibiotic resistance determinants. The occurrence of clinically-important Acinetobacter species suggests possible contamination of these selected rivers which are consumed by humans and livestock, as well as being used for irrigation system, and this constitutes a risk to public health. It also shows that A. baumannii and A. nosocomialis can thrive in the aquatic environment. This study suggests that direct utilization of water from these sources for domestic and other purposes without any form of pre-treatment should be avoided. It is, therefore, necessary for regulatory authorities to monitor the release of domestic and industrial wastewater into these water bodies in order to prevent outbreaks of epidemics. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2019
- Full Text:
- Date Issued: 2019-09
Commensal bacteria belonging to the Staphylococcus Acinetobacter and Stenotrophomonas genera as reservoirs of antibiotic resistance determinants in the environment of Nkonkobe Municipality, Eastern Cape Province , South Africa
- Authors: Adegoke, Anthony Ayodeji
- Date: 2012
- Subjects: Acinetobacter infections , Drug resistance in microorganisms , Staphylococcal infections , Bacterial diseases
- Language: English
- Type: Thesis , Doctoral , Degree
- Identifier: http://hdl.handle.net/10353/6539 , vital:30551
- Description: A study to assess the potentials of some commensal bacteria that belong to Staphylococcus, Acinetobacter and Stenotrophomonas genera as reservoirs of antibiotic resistance determinants in the environment of Nkonkobe Municipality of the Eastern Cape Province, South Africa, was carried out using standard microbiological and molecular techniques. A total of 120 Staphylococcus isolates which consisted of Staphylococcus haemolyticus (30%), Staphylococcus aureus (23.3%) from pig; Staphylococcus capitis (15%) from goat; Staphylococcus heamolyticus (5%) and Staphylococcus xylosus (15%) from cattle and other Staphylococci (11%) from dead chicken and pigs were isolated. About 23.3% of these isolates were coagulase positive and 76.7% were coagulase negative. This difference in prevalence along coagulase production divide was statistically significant (p < 0.05). Eighty-six Acinetobacter species (Acinetobacter baumannii/calcoaceticus and Acinetobacter haemolyticus) were also isolated from Alice and Fort Beaufort towns samples, while 125 Stenotrophomonas maltophilia isolates were from grass root rhizosphere (96%) and soil butternut root rhizosphere (4%). Between 75-100% of the Staphylococccus species were resistant to Penicillin G, tetracycline, sulphamethaxole and nalidixic acid; about 38 % were methicillin resistant, consisting of 12.6% methicillin resistant Staphylococcus aureus (MRSA) from pig and a total of 12% vancomycin resistant were observed. Also, 12% of the isolates were erythromycin resistant while 40.2 % were resistant to the third generation cephalosporin, ceftazidime. The antibiotic resistance genes vanA, VanB, eryA, eryB, eryC were not detected in all the phenotypically resistant Staphylococccus species, but mec A gene and mph genes were detected. In the Acinetobacter species, a wide range of 30-100% resistance to penicillin G, ceftriazone, nitrofurantoin, erythromycin, and augmentin was observed. Polymerase chain reaction (PCR) revealed the presence of Tet(B) and Tet(39) genes in these species, while Tet (A), Tet(M) and Tet(H) were absent. Also, 9.3% of the Acinetobacter species showed phenotypic production of extended spectrum beta lactamases (ESBLs) while 3.5% were positive for the presence of blaCTX-M-1 genes. The Stenotrophomonas maltophilia isolates showed varying resistance to meropenem (8.9%), cefuroxime (95.6 %), ampicillin-sulbactam (53.9%), ceftazidime (10.7%), cefepime (29.3 %), minocycline (2.2%), kanamycin (56.9%), ofloxacin (2.9%), levofloxacin (1.3%), moxifloxacin (2.8%), ciprofloxacin (24.3%), gatifloxacin (1.3%), polymyxin B (2.9 %), cotrimoxazole (26.1%), trimethoprim (98.6%), aztreonam(58%) and Polymyxin B (2.9 %). The isolates exhibited significant susceptibility to the fluoroquinolones (74.3-94.7 %), polymycin (97.1%) and meropenem (88.1%). Only sul3 genes were the only sulphonamide resistance gene detected among the trimethoprim-sulphamethoxazole resistant isolates. The observed multiple antibiotic resistance indeces (MARI) of >2 for Staphylococcus species, Acinetobacter species and Stenotrophomonas maltophilia suggest that they have arisen from high-risk sources where antibiotics are in constant arbitrary use resulting in high selective pressure. The presence of tetracycline resistance genes in Acinetobacter species justifies the observed phenotypic resistance to oxytetracycline and intermediate resistance to minocycline. High phenotypic resistance and the presence of some resistance genes in Staphylococcus species is a possible threat to public health and suggests animals to be important reservoirs of antibiotic resistance determinants in the environment. Indiscriminate use of antibiotics induces this kind of antibiotic resistance and should be discouraged. Personal hygiene is encouraged as it reduces the load of Acinetobacter species contacted from the environment that may be difficult to control. Commensal Stenotrophomonas maltophilia are as important as their clinical counterparts due to their roles in opportunistic infection, antibiotic resistance and their associated genes, especially sul gene. Personal hygiene is hereby advocated especially when in contact with soil, plants and plants’ rhizospheric soil.
- Full Text:
- Date Issued: 2012
- Authors: Adegoke, Anthony Ayodeji
- Date: 2012
- Subjects: Acinetobacter infections , Drug resistance in microorganisms , Staphylococcal infections , Bacterial diseases
- Language: English
- Type: Thesis , Doctoral , Degree
- Identifier: http://hdl.handle.net/10353/6539 , vital:30551
- Description: A study to assess the potentials of some commensal bacteria that belong to Staphylococcus, Acinetobacter and Stenotrophomonas genera as reservoirs of antibiotic resistance determinants in the environment of Nkonkobe Municipality of the Eastern Cape Province, South Africa, was carried out using standard microbiological and molecular techniques. A total of 120 Staphylococcus isolates which consisted of Staphylococcus haemolyticus (30%), Staphylococcus aureus (23.3%) from pig; Staphylococcus capitis (15%) from goat; Staphylococcus heamolyticus (5%) and Staphylococcus xylosus (15%) from cattle and other Staphylococci (11%) from dead chicken and pigs were isolated. About 23.3% of these isolates were coagulase positive and 76.7% were coagulase negative. This difference in prevalence along coagulase production divide was statistically significant (p < 0.05). Eighty-six Acinetobacter species (Acinetobacter baumannii/calcoaceticus and Acinetobacter haemolyticus) were also isolated from Alice and Fort Beaufort towns samples, while 125 Stenotrophomonas maltophilia isolates were from grass root rhizosphere (96%) and soil butternut root rhizosphere (4%). Between 75-100% of the Staphylococccus species were resistant to Penicillin G, tetracycline, sulphamethaxole and nalidixic acid; about 38 % were methicillin resistant, consisting of 12.6% methicillin resistant Staphylococcus aureus (MRSA) from pig and a total of 12% vancomycin resistant were observed. Also, 12% of the isolates were erythromycin resistant while 40.2 % were resistant to the third generation cephalosporin, ceftazidime. The antibiotic resistance genes vanA, VanB, eryA, eryB, eryC were not detected in all the phenotypically resistant Staphylococccus species, but mec A gene and mph genes were detected. In the Acinetobacter species, a wide range of 30-100% resistance to penicillin G, ceftriazone, nitrofurantoin, erythromycin, and augmentin was observed. Polymerase chain reaction (PCR) revealed the presence of Tet(B) and Tet(39) genes in these species, while Tet (A), Tet(M) and Tet(H) were absent. Also, 9.3% of the Acinetobacter species showed phenotypic production of extended spectrum beta lactamases (ESBLs) while 3.5% were positive for the presence of blaCTX-M-1 genes. The Stenotrophomonas maltophilia isolates showed varying resistance to meropenem (8.9%), cefuroxime (95.6 %), ampicillin-sulbactam (53.9%), ceftazidime (10.7%), cefepime (29.3 %), minocycline (2.2%), kanamycin (56.9%), ofloxacin (2.9%), levofloxacin (1.3%), moxifloxacin (2.8%), ciprofloxacin (24.3%), gatifloxacin (1.3%), polymyxin B (2.9 %), cotrimoxazole (26.1%), trimethoprim (98.6%), aztreonam(58%) and Polymyxin B (2.9 %). The isolates exhibited significant susceptibility to the fluoroquinolones (74.3-94.7 %), polymycin (97.1%) and meropenem (88.1%). Only sul3 genes were the only sulphonamide resistance gene detected among the trimethoprim-sulphamethoxazole resistant isolates. The observed multiple antibiotic resistance indeces (MARI) of >2 for Staphylococcus species, Acinetobacter species and Stenotrophomonas maltophilia suggest that they have arisen from high-risk sources where antibiotics are in constant arbitrary use resulting in high selective pressure. The presence of tetracycline resistance genes in Acinetobacter species justifies the observed phenotypic resistance to oxytetracycline and intermediate resistance to minocycline. High phenotypic resistance and the presence of some resistance genes in Staphylococcus species is a possible threat to public health and suggests animals to be important reservoirs of antibiotic resistance determinants in the environment. Indiscriminate use of antibiotics induces this kind of antibiotic resistance and should be discouraged. Personal hygiene is encouraged as it reduces the load of Acinetobacter species contacted from the environment that may be difficult to control. Commensal Stenotrophomonas maltophilia are as important as their clinical counterparts due to their roles in opportunistic infection, antibiotic resistance and their associated genes, especially sul gene. Personal hygiene is hereby advocated especially when in contact with soil, plants and plants’ rhizospheric soil.
- Full Text:
- Date Issued: 2012
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