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Isolation and polymerase chain reaction identification of bacteria from the 2014–2015 flood of Kota Bharu, Kelantan, Malaysia

Pwaveno Huladeino Bamaiyi
Pwaveno Huladeino Bamaiyi
, 
Mohd Sani Nani Izreen
Mohd Sani Nani Izreen
, 
Khatijah Mohamad
Khatijah Mohamad
, 
Badrul Hisham Nur Eizzati
Badrul Hisham Nur Eizzati
, 
Che Rostman Siti-Bainum
Che Rostman Siti-Bainum
, 
Mat Kamir Norsyamimi Farhana
Mat Kamir Norsyamimi Farhana
, 
Mohd Nor Mohd Norfaizull
Mohd Nor Mohd Norfaizull
, 
Saeid Kadkhodaei
Saeid Kadkhodaei
 and 
Goriman Khan Mohd Azam Khan
Goriman Khan Mohd Azam Khan
   | Mar 31, 2017
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Article Category: Original article
Published Online: Mar 31, 2017
Page range: 549 - 565
DOI: https://doi.org/10.5372/1905-7415.1006.525
Keywords
© 2016 Pwaveno Huladeino Bamaiyi, Mohd Sani Nani Izreen, Khatijah Mohamad, Badrul Hisham Nur Eizzati, Che Rostman Siti-Bainum, Mat Kamir Norsyamimi Farhana, Mohd Nor Mohd Norfaizull, Saeid Kadkhodaei, Goriman Khan Mohd Azam Khan
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Trimming using Geneious version R8.1 (Biomatters, http://www.geneious.com, Kearse et al. [10])
Trimming using Geneious version R8.1 (Biomatters, http://www.geneious.com, Kearse et al. [10])

Figure 2

Capping using Geneious version R8.1 (Biomatters, http://www.geneious.com, Kearse et al. [10])
Capping using Geneious version R8.1 (Biomatters, http://www.geneious.com, Kearse et al. [10])

Figure 3

PCR results on gel electrophoresis are shown isolates 1a1 to 1d2
PCR results on gel electrophoresis are shown isolates 1a1 to 1d2

Figure 4

PCR results on gel electrophoresis are shown isolates 1e1 to 3d2
PCR results on gel electrophoresis are shown isolates 1e1 to 3d2

Figure 5

PCR results on gel electrophoresis are shown isolates 3d3 to 4d3
PCR results on gel electrophoresis are shown isolates 3d3 to 4d3

Figure 6

PCR results on gel electrophoresis are shown isolates 4e1 to 6x2
PCR results on gel electrophoresis are shown isolates 4e1 to 6x2

Figure 7

Chromobacterium violaceum confirmed by species specific PCR for isolates 2d1 and 3d1
Chromobacterium violaceum confirmed by species specific PCR for isolates 2d1 and 3d1

Figure 8

Preprocessed 16S rRNAamplicon data submitted to the Ribosomal Database Project Database Classifier (Wang et al. [11]) and visualized using the Krona Interactive Hierarchical Browser (Ondov et al. [13]).
Preprocessed 16S rRNAamplicon data submitted to the Ribosomal Database Project Database Classifier (Wang et al. [11]) and visualized using the Krona Interactive Hierarchical Browser (Ondov et al. [13]).

Figure 9

Antibiotic resistance plot showing the mean resistance of various antibiotics tested
Antibiotic resistance plot showing the mean resistance of various antibiotics tested

Analysis of variance of antibiotics sensitivity (multiple comparisons) with Tukey honest significant difference post hoc test

(I) Antibiotic(J) AntibioticsMean Difference (I–J)Std. ErrorP95% Confidence Interval
     LowerUpper
TE 30–tetracyclineAML 10–amoxycillin5.473.090.57–3.7914.73
S 25–streptomycin1.823.09>0.99–7.4411.09
CN 10–gentamycin–2.533.090.98–11.796.73
E 15–erythromycin0.713.09>0.99–8.569.97
AMP 10–ampicillin9.59

P<0.05;

3.090.040.3318.85
P 10–penicilling11.77

P<0.01;

3.090.0042.5021.03
AML 10–amoxycillinTE 30–tetracycline–5.473.090.57–14.733.79
S 25–streptomycin–3.653.090.90–12.915.62
CN 10–gentamycin–8.003.090.14–17.261.26
E 15–erythromycin–4.773.090.72–14.034.50
AMP 10–ampicillin4.123.090.83–5.1413.38
P 10–penicilling6.293.090.40–2.9715.56
S 25–streptomycinTE 30–tetracycline–1.823.09>0.99–11.097.44
AML 10–amoxycillin3.653.090.90–5.6212.91
CN 10–gentamycin–4.353.090.80–13.624.91
E 15–erythromycin–1.123.09>0.99–10.388.14
AMP 10–ampicillin7.773.090.16–1.5017.03
P 10–penicilling9.94

P<0.05;

3.090.030.6819.20
CN 10–gentamycinTE 30–tetracycline2.533.090.98–6.7311.79
AML 10–amoxycillin8.003.090.14–1.2617.26
S 25–streptomycin4.353.090.80–4.9113.62
E 15–erythromycin3.243.090.94–6.0312.50
AMP 10–ampicillin12.12

P<0.01;

3.090.0032.8621.38
P 10–penicilling14 29

P<0.001.F = 5.875; η = 0.239

3.090.0015.0323.56
E 15–erythromycinTE 30–tetracycline–0.713.090.99–9.978.56
AML 10–amoxycillin4.763.090.72–4.5014.03
S 25–streptomycin1.123.090.99–8.1410.38
CN 10–gentamycin–3.243.090.94–12.506.03
AMP 10–ampicillin8.883.090.070.3818.14
P 10–penicilling11.06

P<0.05;

3.090.0091.8020.32
AMP 10–ampicillinTE 30–tetracycline–9.59

P<0.05;

3.090.04–18.85–0.33
AML 10–amoxycillin–4.123.090.83–13.385.14
S 25–streptomycin–7.763.090.16–17.031.50
CN 10–gentamycin–12.12

P<0.01;

3.090.003–21.38–2.86
E 15–erythromycin–8.883.090.07–18.140.38
P 10– penicillin G2.183.09>0.99–7.0911.44
P 10–penicillin GTE 30–tetracycline–11.76

P<0.01;

3.090.004–21.03–2.50
AML 10–amoxycillin–6.293.090.40–15.562.97
S 25–streptomycin–9.94

P<0.05;

3.090.03–19.20–0.68
CN 10–gentamycin–14 29

P<0.001.F = 5.875; η = 0.239

3.090.001–23.56–5.03
E 15–erythromycin–11.06

P<0.01;

3.090.009–20.32–1.80
AMP 10–ampicillin–2.183.090.99–11.447.09

Bacteria Identified to species level from the flood and deposited at the GenBank

S/No.Submission IDAccession NumberBacteria Identified
1SUB882316 UMK1a1KR027927Staphylococcus xylosus
2SUB882316 UMK1a2KR027928Acinetobacter ursingii
3SUB882316 UMK1b1KR027929Aeromonas aquariorum (A. dhakensis)
4SUB882316 UMK1b2KR027930Bacillus pseudofirmus
5SUB882316 UMK1b3KR027931Bacillus altitudinis
6SUB882316 UMK1c2KR027932Acinetobacter radioresistens
7SUB882316 UMK1d1KR027933Acinetobacter radioresistens
8SUB882316 UMK1d2KR027934Lactococcus lactis subsp. Lactis
9SUB1092331 UMK1e1KT731961Acidovorax caeni
10SUB1092331 UMK1e2KT731962Acidovorax caeni
11SUB882316 UMK2a1KR027935Staphylococcus xylosus
12SUB1092331 UMK2a2KT731963Acidovorax caeni
13SUB882316 UMK2a3KR027936Aeromonas veronii
14SUB1092331 UMK2d1KT731964Chromobacterium violaceum
15SUB882316 UMK2e1KR027937Staphylococcus xylosus
16SUB882316 UMK2e2KR027938Aeromonas veronii
17SUB882316 UMK3a1KR027939Acinetobacter junii
18SUB882316 UMK3a2KR027940Klebsiella pneumoniae subsp. Rhinoscleromatis
19SUB882316 UMK3a3KR027941Raoultella terrigena
20SUB882316 UMK3b1KR027942Pseudomonas trivialis
21SUB1092331 UMK3b2KT731965Curvibacter gracilis
22SUB882316 UMK3b3KR027943Pseudomonas veronii
23SUB1092331 UMK3c3KT731966Rhodococcus equi
24SUB1092331 UMK3d2KT731967Chromobacterium violaceum
25SUB882316 UMK3d3KR027944Bacillus megaterium
26SUB1092331 UMK3d4KT731968Aquitalea magnusonii
27SUB1092331 UMK3d5KT731969Wautersia numazuensis (Cupriavidus numazuensis)
28SUB882316 UMK3e1KR027945Exiguobacterium acetylicum
29SUB882316 UMK3e2KR027946Chryseobacterium gambrini
30SUB883111 UMK4a1wKR048048Salmonella enterica subsp. Diarizonae
31SUB883111 UMK4a1yKR048049Bacillus idriensis
32SUB883111 UMK4a2KR048050Staphylococcus xylosus
33SUB882316 UMK4b1KR027947Aeromonas aquariorum (A dhakensis)
34SUB882316 UMK4b2KR027948Pectobacterium cypripedii (Pantoea cypripedii)
35SUB882316 UMK4b3KR027949Pseudomonas trivialis
36SUB882316 UMK4c2KR027950Bacillus luciferensis
37SUB882316 UMK4c3KR027951Enterobacter asburiae
38SUB882316 UMK4d2KR027952Bacillus luciferensis
39SUB882316 UMK4d3KR027953Aeromonas aquariorum (A dhakensis)
40SUB882316 UMK4e1KR027954Acinetobacter calcoaceticus
41SUB882316 UMK4e2KR027955Bacillus pseudofirmus
42SUB882316 UMK5a1KR027956Proteus mirabilis
43SUB882316 UMK5a2KR027957Escherichia coli
44SUB882316 UMK5b1KR027958Exiguobacterium mexicanum
45SUB882316 UMK5d1KR027959Bacillus luciferensis
46SUB883111 UMK6a1wKR048051Staphylococcus xylosus
47SUB883111 UMK6a1yKR048052Bacillus pseudofirmus
48SUB1092331 UMK6a2KT731970Acinetobacter calcoaceticus
49SUB1092331 UMK6b1KT731971Rubrivivax gelatinosus
50SUB1092331 UMK6b2KT731972Acidovorax caeni
51SUB1092331 UMK6cKT731973Acidovorax caeni
52SUB882316 UMK6dKR027960Raoultella terrigena
53SUB882316 UMK6eKR027961Pseudomonas vranovensis
54SUB1092331 UMK6x1KT731974Acidovorax caeni
55SUB1092331 UMK6x2KT731975Acidovorax caeni

Antibiotic sensitivity test of some bacteria isolates from the flood

No.Isolate (bacteria)TE 30-tetracyclineAML 10– amoxycillinS 25 – streptomycinCN 10– gentamycinE 15– erythromycinAMP 10– ampicillinP10– penicillin G% Total resistance to all antibiotics
12dl (Chromobacterium violaceum)31 (S)R15 (I)19 (S)20 (I)RR43%
23a2 (Klebsiella pneumoniae subsp. Rhinoscleromatis)25 (S)R11 (R)19 (S)12 (R)RR71%
33a3 (Raoultella terrigena)22 (S)12 (R)15 (I)19 (S)11 (R)RR57%
44b3 (Pseudomonas trivialis)16 (I)R20 (I)20 (S)24 (S)RR43%
54d2 (Bacillus luciferensis)28 (S)13 (R)23 (S)25 (S)30 (S)12 (I)R29%
64d3 (Aeromonas aquariorum)21 (S)27 (S)18 (I)22 (S)15 (I)RR29%
74e2 (Bacillus pseudofirmus)12 (R)20 (S)21 (S)25 (S)23 (S)R22 (S)29%
85a2 (Escherichia coli)14 (R)15 (I)12 (R)18 (S)12 (R)17 (S)R57%
95b 1 (Exiguobacterium mexicanum)26 (S)40 (S)22 (S)25 (S)28 (S)44 (S)30 (S)0%
105dl (Bacillus luciferensis)21 (S)22 (S)20 (I)25 (S)19 (I)20 (S)12 (R)14%
116a lw (Staphylococcus xvlosus)20 (S)13 (R)22 (S)24 (S)15 (I)12 (R)R43%
126a ly (Bacillus pseudofirmus)22 (S)R17 (I)18 (S)23 (S)RR43%
136a2 (Acinetobacter calcoaceticus)25 (S)31 (S)25 (S)31 (S)28 (S)31 (S)28 (S)0%
146b 1 (Rubrivivax gelatinosus)23 (S)R20 (I)33 (S)13 (R)RR57%
156b2 (Acidovorax caeni)11 (R)17 (I)18 (I)22 (S)25 (S)R18 (S)29%
166c (Acidovorax caeni)12 (R)12 (R)18 (I)25 (S)26 (S)12 (I)7 (R)43%
176e (Pseudomonas vranovensis)23 (S)32 (S)24 (S)25 (S)16 (I)32 (S)25 (S)0%
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