Participants’ demographic characteristics
Two hundred twenty five patients’ record were reviewed. Nine patients were excluded due to mixed culture growths or contaminated samples. Two hundred sixteen participants were recruited and all included in the final analysis as illustrated in Fig. 1.
Among the 216 participants, the majority 133(61.57%) were males. The mean age of the participants was 54.93 ± 14.48 years. Majority of the participants, 119(53.72%) were from private facilities, Table 1.
Table 1
Participants’ characteristics
Variable
|
n (%)
|
Sex n = 216
|
|
Female
|
83(38.43)
|
Male
|
133(61.57)
|
Age-range n = 216
|
|
≤ 30
|
09(4.17)
|
31–40
|
36(16.67)
|
41–50
|
44(20.37)
|
51–60
|
25(11.57)
|
> 60
|
102(47.22)
|
Facility type n = 216
|
|
Government
|
97(44.91)
|
Private
|
119(55.09)
|
Initial empirical Broad spectrum antibiotics n = 216
|
|
Yes
|
216(100)
|
No
|
0(0)
|
Characteristics Of Samples Taken For Cultures And Sensitivity
Majority of the participants, 170(78.70%) had samples taken off from one source; either blood, tracheal aspirate, urine or pus swab. Majority of the participants 75(34.72%) had tracheal related samples only taken off for culture and sensitivity. This was followed by urine in 50(23.15%) and then venous blood in 46(21.30%) as detailed in Table 2.
Table 2
Sample source n = 216
|
n (%)
|
Venous blood only
|
46(21.30)
|
Tracheal aspirate/sputum/Endotracheal catheter tip
|
75(34.72)
|
Urine
|
50(23.15)
|
Urinary catheter tip
|
4(1.85)
|
Pus swab
|
5(2.31)
|
Urine and Urinary catheter tip
|
1(0.46)
|
Venous blood and urine
|
5(2.31)
|
Venous blood, urine and urinary catheter tip
|
1(0.46)
|
Venous blood and tracheal aspirate
|
15(6.94)
|
Venous blood, tracheal aspirate and urine
|
14(6.48)
|
Outcome Of Culture And Gram Stain
About 111(51.39%) of the samples reviewed were culture positive. On gram staining, about 58(52.25%) were gram positive and 53(47.75%) were gram negative. Among those that were gram positive, 31(54.39%) were gram positive oval yeast cells. The majority of the isolates, 80(74.07%) were of bacterial kingdom. All the fungi isolated 31(100%) were Candida albicans. Among the gram positive cocci, staphylococcal spices constituted the majority 24(96.00%) of the isolated bacteria. Among the staphylococcal spices, Staphylococci aureus was the majority in 23(95.83%) samples. All the gram negative organisms isolated were rods among which, Citrobacter freudii constituted the majority 19(35.19%). This was followed by Pseudomonas aureginosa 15(27.78%), Klebsiella pneumonia 10(18.52%), and Escherichia coli 08(14.81%) as detailed in Table 3.
Table 3
Culture and gram stain results
Variable
|
n (%)
|
Growth n = 216
|
|
Had no Growth
|
105(48.61)
|
Had Growth
|
111(51.39)
|
Gram stain n = 111
|
|
Gram positive
|
58(52.25)
|
Gram negative
|
53(47.75)
|
Gram positive n = 57
|
|
Gram positive oval yeast cell
|
31(54.39)
|
Gram positive cocci
|
26(45.61)
|
Organism isolated n = 108
|
|
Bacteria
|
80(72.07)
|
Fungi
|
31(27.93)
|
Fungi n = 31
|
|
Candida albicans
|
31(100)
|
Others
|
0(0)
|
Gram positive cocci n = 25
|
|
Staphylococci
|
24(96.00)
|
Streptococci
|
01(4.00)
|
Staphylococci n = 24
|
|
Staphylococci aureus
|
23(95.83
|
Staphylococcus saprophyticus
|
01(4.17)
|
Streptococci n = 01
|
|
Streptococci viridians
|
01(100)
|
Others
|
0(0)
|
Gram positive organisms n = 25
|
|
Staphylococci aureus
|
23(92.00)
|
Staphylococcus saprophyticus
|
01(4.00)
|
Streptococci viridians
|
01(4.00)
|
Gram negative Rods n = 54
|
|
Escherichia coli
|
08(14.81)
|
Citrobacter freudii
|
19(35.19)
|
Pseudomonas aureginosa
|
15(27.78)
|
Klebsiella pneumonia
|
10(18.52)
|
Proteus mirabillis
|
01(1.85)
|
Acinetobacter spp
|
01(1.85)
|
Bacterial Species Isolated And Corresponding Sources
Staphylococcus aureus 23(28.75%), Citrobacter freudii 19(23.75%), Pseudomonas aureginosa 15(18.75%) and Klebsiella pneumoniae 10(12.50%) were the most frequently isolated bacterial species. The only Acinetobacter spp isolated 1(1.25%) was from blood. Most of the Staphylococcus aureus isolated 15(60%) were from blood while majority 12(30.77%) of Citrobacter freudii, Pseudomonas aureginosa 09(23.08%) and Klebsiella pneumoniae 06(15.38%) were isolated from the trachea. Most of the Escherichia coli isolated were from urine 05(41.67%). Details of the bacterial species isolated and their corresponding sources are as shown in Table 4.
Table 4
Bacterial species and their sources
Bacterial spices
|
No. of Isolates
n (%)
|
Sample
|
|
|
|
Blood
n (%)
|
Tracheal Aspirate
n (%)
|
Urine
n (%)
|
Catheter tip
n (%)
|
Pus swab
n (%)
|
Staphylococcus aureus
|
23(28.75)
|
15(60.00)
|
08(20.51)
|
0(0)
|
0(0)
|
0(0)
|
Escherichia coli
|
8(10.00)
|
01(4.00)
|
02(5.13)
|
05(41.67)
|
0(0)
|
0(0)
|
Citrobacter freudii
|
19(23.75)
|
04(16.00)
|
12(30.77)
|
03(25.00)
|
0(0)
|
0(0)
|
Pseudomonas aureginosa
|
15(18.75)
|
01(4.00)
|
09(23.08)
|
02(16.67)
|
01(100)
|
02(66.67)
|
Klebsiella pneumoniae
|
10(12.50)
|
03(12.00)
|
06(15.38)
|
01(8.33)
|
0(0)
|
0(0)
|
Others
|
05(6.25)
|
01(4.000)
|
2(5.13)
|
01(8.33)
|
0(0)
|
01(33.33)
|
Total n (%)
|
80(100)
|
24(100)
|
39(100)
|
12(100)
|
01(100)
|
03(100)
|
Note: Others include; Acinetobacter spp, Staphylococcus saprophyticus, Streptococci viridians, Leuconostoc mesentero and Proteus mirabilis |
Categorization Of Co-infections And Sensitivity Results
The prevalence of co-infections among COVID-19 ICU patients in this study was found to be 111(51.39%)
Respiratory tract infection was the most prevalent, 55(51.89%) followed by primary blood stream infection and urinary tract infections which both share the same prevalence of 23(21.70%) as shown in Table 5. About 07/80(8.75%) of the bacterial species were extended spectrum beta lactamase or AmpC beta lactamase producers. Five, 05(71.43%) of the Klebsiella pneumoniae were ESBL producers, 01(14.29%) was both ESBL and Carbapenase producers and 01(14.29%) was a Penicillinase producer. Also about 02(66.67%) of Pseudomonas aureginosa were carbapenemase and HL producer and 01(3.33%) was both ESBL and Carbapemase producer. Only 1 (one) of the Proteus mirabilis was Penicillinase producer, About 04(40%) of Klebsiella pneumonia were HL AMPC gene expressers as shown in Table5. A total of 60(75.95%) of the organisms demonstrated at least one form of drug resistance. Among these organisms, about 48(80%) demonstrated multidrug resistance and 12(20%) were labeled as possible extensive drug resistant as detailed in Table 5.
Table 5
Categorization of infections and sensitivity results
Variable
|
n (%)
|
Co-infection n = 216
|
|
No infection
|
105(48.61)
|
Has infection
|
111(51.39)
|
Types of infections n = 111
|
|
Respiratory tract infection
|
57(51.35)
|
Urinary tract infection
|
25(22.52)
|
Primary blood stream infections
|
24(21.62)
|
Catheter colonization
|
01(0.90)
|
Wound colonization
|
03(2.70)
|
Others
|
01(0.90)
|
Enzyme production n = 11
|
|
ESBL producer
|
05(45.45)
|
Both ESBL and Carbapenemase producers
|
02(18.18)
|
Penicillinase producer
|
02(18.18)
|
Carbapenemase and HL cephalosporin producers
|
02(18.18)
|
Gene Expression n = 5
|
|
HL AMPC gene
|
05(100)
|
Drug resistance n = 79
|
|
No drug resistance
|
19(24.05)
|
Has drug resistance
|
60(75.95)
|
Types of drug resistance n = 60
|
|
Multidrug resistance
|
48(80.00)
|
Possible Extensive drug resistance
|
12(20.00)
|
Overall Susceptibility Of Bacterial Species Isolated From The Participants
Escherichia coli demonstrated the highest susceptibility to Augmentin 6/7(85.71%). This was followed by Staphylococcus aureus 16/19(84.21%). Klebsiella pneumonia 2/8(25.00%) and Pseudomonas aureginosa 0/4(0%) showed the lowest susceptibility to Augmentin, details are showed in Table 6:
Table 6
Overall Susceptibility of bacterial species isolated from the participants
|
Bacteria Species
|
|
No. susceptible/total number tested (%)
|
Antibiotic
|
A.spp
|
S.aureus
|
S.saprophyticus
|
S.viridans
|
E.coli
|
C.freudii
|
P.aureginosa
|
K.pneumoniae
|
L.mesentero
|
P.mirabilis
|
Ampicillin
|
-
|
0/2(0)
|
-
|
-
|
-
|
0/1(0)
|
0/4(0)
|
1/7(14.29)
|
-
|
0/1(1)
|
Augmentin
|
-
|
16/19(84.21)
|
-
|
-
|
6/7(85.71)
|
8/15(53.33)
|
0/4(0)
|
2/8(25.00)
|
-
|
1/1(100)
|
Ampicillin/
Sulbactum
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
0/4(0)
|
1/7(14.29)
|
-
|
1/1(100)
|
PISA
|
0/1(0)
|
-
|
-
|
-
|
-
|
1/1(100)
|
0/4(0)
|
1/6(16.67)
|
-
|
1/1(100)
|
Cefazoline
|
-
|
-
|
-
|
-
|
-
|
-
|
0/4(0)
|
2/7(28.57)
|
-
|
1/1(100)
|
Cefuroxime
|
-
|
4/14(28.57)
|
-
|
-
|
0/3(0)
|
0/5(0)
|
0/4(0)
|
2/7(28.57)
|
-
|
0/1(0)
|
Cefuroxime Axetil
|
-
|
-
|
-
|
-
|
-
|
-
|
0/4(0)
|
2/7(28.57)
|
-
|
0/1(100)
|
Cefoxitine
|
-
|
-
|
-
|
-
|
-
|
-
|
0/4(0)
|
3/7(42.86)
|
-
|
0/1(0)
|
Cefotaxime
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
0/4(0)
|
2/7(28.57)
|
-
|
1/1(100)
|
Ceftazidine
|
0/1(0)
|
-
|
-
|
-
|
0/2(0)
|
0/5(0)
|
4/8(50)
|
1/7(14.29)
|
-
|
1/1(100)
|
Ceftriaxone
|
-
|
0/10(0)
|
-
|
-
|
0/5(0)
|
2/14(14.29)
|
0/4(0)
|
8/10(80)
|
-
|
0/1(0)
|
Cefepime
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/4(0)
|
2/7(28.57)
|
-
|
1/1(100)
|
Aztreonam
|
-
|
0/2
|
-
|
-
|
-
|
-
|
0/6(0)
|
1/6(16.67)
|
-
|
1/1(100)
|
Meropenem
|
-
|
-
|
-
|
-
|
-
|
-
|
0/4(0)
|
3/7(42.86)
|
-
|
1/1(100)
|
Imipenem
|
0/1(0)
|
-
|
-
|
-
|
6/6(100)
|
10/16(62.50)
|
1/12(8.33)
|
3/4(75)
|
-
|
-
|
Amikacin
|
1/1(100)
|
-
|
-
|
-
|
-
|
1/1(100)
|
0/4(0)
|
4/7(57.14)
|
-
|
1/1(100)
|
Gentamycin
|
0/1(0)
|
5/11(45.45)
|
1/1(100)
|
-
|
3/3(100)
|
3/16(18.75)
|
1/15(6.67)
|
4/10(40)
|
0/1(100)
|
1/1(100)
|
Ciprofloxacin
|
0/1(0)
|
4/15(26.67)
|
-
|
-
|
1/7(14.29)
|
4/18(22.22)
|
0/13(0)
|
5/10(0)
|
-
|
1/1(100)
|
Nitrofuratoin
|
-
|
1/1(100)
|
0/1(0)
|
-
|
5/5(100)
|
1/2(50)
|
0/4(0)
|
1/7(14.29)
|
1/1(100)
|
0/1(0)
|
Contrimoxazole
|
-
|
2/4(50)
|
1/1(100)
|
-
|
0/2(0)
|
2/5(40)
|
0/4(0)
|
3/7(42.86)
|
1/1(100)
|
0/1(0)
|
Sulfamethazole
|
-
|
2/4(50)
|
-
|
-
|
0/1(0)
|
1/4(25.00)
|
-
|
-
|
-
|
-
|
Chloramphenicol
|
-
|
9/20(45)
|
1/1(100)
|
-
|
3/4(75
|
5/10(50)
|
-
|
1/3(33.33)
|
1/1(100)
|
-
|
Benzylpenicilline
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
-
|
Oxacilline
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
-
|
Tobramycin
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
0/1(0)
|
-
|
Levofloxacin
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
Moxifloxacin
|
-
|
-
|
1/1(100)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
|
nalidixic acid
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
|
Erythromycin
|
-
|
0/4(0)
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
-
|
Clindamycin
|
-
|
6/12(50)
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
|
Linezolid
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
polymyxin B
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
Teicoplanin
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
Vancomycin
|
-
|
12/12(100)
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
Tetracycline
|
-
|
8/9(88.89)
|
0/1(0)
|
-
|
1/1(100)
|
0/4(0)
|
-
|
-
|
0/1(0)
|
-
|
Tigecycline
|
-
|
1/1(100)
|
1/1(100)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
Fosfomycin
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
-
|
Rifampicin
|
-
|
-
|
1/1(100)
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
Mupirocin
|
-
|
-
|
0/1(0)
|
-
|
-
|
-
|
-
|
-
|
0/1(0)
|
-
|
Piperacilin
|
-
|
-
|
-
|
-
|
-
|
-
|
1/4(25)
|
-
|
-
|
-
|
Ertapenem
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
-
|
-
|
Colistin
|
-
|
-
|
-
|
-
|
-
|
1/1(100)
|
11/11(100)
|
1/1(100)
|
-
|
-
|
Note: A.spp- Acinetobacter spp, S.aureus- Staphylococcus aureus, S.saprophyticus- Staphylococcus saprophyticus, S.viridans - Streptoccoci viridans, E.coli- Escherichia coli, C.freudii- Citrobacter freudii, P.aureginosa- Pseudomonas aureginosa, K.pneumoniae- Klebsiella pneumonia, L.mesentero- Leuconostoc mesentero, P.mirabilis- Proteus mirabilis |
Multidrug Resistant Bacterial Species Isolated From The Participants
The prevalence of multidrug resistance in this study was 75.95%. Majority, 7/10(70%) of Klebsiella pneumoniae were found to be multidrug resistant. Majority of the Staphylococcus aureus 15(65.22%) were multidrug resistant. The majority, 16/19(84.21%) of Citrobacter freudii and 13/15(86.67%) of Pseudomonas aureginosa demonstrated multidrug resistance, details are shown in Table 7.
Table 7
Multidrug resistant bacterial species isolated from the participants
Organism
|
No. of MDR isolates/Total no. of isolates
|
% of isolates that were MDR
|
Acinetobacter spp
|
01/1
|
100
|
Staphylococci aureus
|
15/23
|
65.22
|
Staphylococcus saprophyticus
|
01/1
|
100
|
Escherichia coli
|
05/8
|
62.50
|
Citrobacter freudii
|
16/19
|
84.21
|
Pseudomonas aureginosa
|
13/15
|
86.67
|
Klebsiella pneumoniae
|
07/10
|
70
|
Leuconostoc mesenteroid
|
01/1
|
100
|
Proteus mirabilis
|
01/1
|
100
|
Overall
|
60/79
|
75.95
|
Extensive Resistant Bacterial Species Isolated From The Participants
The prevalence of possible extended drug resistance was 13/79(16.46%). About five isolates of Klebsiella pneumonia, four isolates of Pseudomonas aureginosa, two isolates of Citrobacter freudii, one isolate of Staphylococcus saprophyticus and one isolate of Acinetobacter spp were labeled as possible extended drug resistant organisms.
Co-fungal Infections Among The Participants
About 31(27.93%) of the organisms isolated were Candida albicans. A few of them were tested for their susceptibility to the different antifungal agents, Table 8.
Susceptibility of Candida albicans to various antifungal agents
Candida albicans, the fungi isolated was susceptible to most antifungal agents, Table 8
Table 8
Susceptibility of Candida albicans to various antifungal agents
|
Candida albicans
|
Anfungal agent
|
No. susceptible/total number tested (%)
|
Ketoconazole
|
02/2(100)
|
Nystatin
|
01/2(50)
|
Amphotericin
|
02/2(100)
|
Flucytosin
|
02/2(100)
|
Econazole
|
02/2(100)
|
Clotrimazole
|
01/2(50)
|
Miconazole
|
02/2(100)
|
itraconazole
|
02/2(100)
|
Voriconazole
|
02/2(100)
|
Fluconazole
|
02/3(66.67)
|
Overall Susceptibility Patterns Of Organisms Isolated Among The Participants
Among antibiotics that had at least 4 isolates tested for susceptibility against. Amoxclave which had 6/10(60%) different species of isolates tested against had the highest overall susceptibility that is 33/54(61.11%). This was followed by tetracycline 9/16(56.25%), chloramphenicol and imipenem which shared the same proportion, 20/39(51.28%), and then amikacin, 7/14(50%) overall susceptibility. Ceftriaxone had the lowest overall susceptibility 4/44(9.09%) among antibiotics that had at least 4 isolates tested for susceptibility against. The results of the overall susceptibility is shown in the Fig. 2 below.