Demographic and clinical characteristics of patients with GNB infections
In this study, 49 (40.8%) of 120 severely ill COVID-19 patients had GNB infections. Of these, the majority were: adults aged above 60 years (36.7%), males (53.1%), married (73.5%), not vaccinated against COVID-19 (77.6%), comorbid (77.6%), and discharged (77.6%) after hospitalization for 6–10 days (51%), Table 2.
Table 2
Demographic and clinical characteristics of patients with GNB infections
Factors
|
Frequency, n = 49
|
Percent (%)
|
Age (years)
|
Median (IQR)
|
49 (32–65)
|
<=24
|
5
|
10.2
|
25–44
|
12
|
24.5
|
45–59
|
14
|
28.6
|
>=60
|
18
|
36.7
|
Gender
|
Male
|
26
|
53.1
|
Female
|
23
|
46.9
|
Marital status
|
Single
|
13
|
26.5
|
Married
|
36
|
73.5
|
Presence of comorbidity
|
Yes
|
38
|
77.6
|
No
|
11
|
22.4
|
SARS-CoV-2 Vaccination status
|
Yes
|
11
|
22.4
|
No
|
38
|
77.6
|
Hospitalization outcome
|
Discharged
|
38
|
77.6
|
Died
|
11
|
22.4
|
Length of hospital stay (Days)
|
Median (IQR)
|
9(5–12)
|
Short stay (0–5)
|
11
|
22.4
|
Medium stay (6–10)
|
25
|
51.0
|
Long stay (> 10)
|
13
|
26.5
|
IQR interquartile range, SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2
Spectrum Of Esbl-producing Gnb Isolates In Covid-19 Patients Admitted To Knh-idu
In this study, 49 out of 120 patients had GNB infections (40.8%). Of these, 33 (67.3%) were caused by ESBL – producers, predominated by Klebsiella pneumoniae (45.5%), Enterobacter cloacae complex (21.2%), Acinetobacter baumannii (12.1%), Escherichia coli (9.1%), Pseudomonas aeruginosa (6.1%) and Enterobacter cloacae (6.1%) Fig. 1. All Enterobacter cloacae complex (100%, 7/7) isolates were ESBL producers, whilst the other GNB isolates, including Proteus mirabilis, Acinetobacter calcoaceticus, Serratia marcescens and Stenotrophomonas maltophilia, were all non-ESBL producers Fig. 1.
Amr Genes Carriage In Esbl-producing Gnb Isolates From Covid-19 Patients Admitted To Knh-idu
We determined the occurrence of the most common ESBL genes, including CTX-M-type, TEM-type, SHV-type, and OXA-1, among the ESBL-producing bacterial isolates. All these genes were present in Klebsiella pneumoniae, predominated by CTX-M-type (60.9%, 14/23), and except for isolate 3OP harboring SHV gene only, other isolates encoded CTX-M-type genes, Fig. 2a. In Enterobacter cloacae complex, CTX-M-type and TEM were the principal ESBL genes (75%, 12/16), and similar to K. pneumoniae, AMR genes were present in all the ESBL-producing isolates, with OXA-1 genes as the minority, Fig. 2b. Fifty per cent (1/2) of ESBL-producing- Enterobacter cloacae isolates harbored a single ESBL gene, TEM, (Fig. 2c). About 67% (2/3) of ESBL-producing E. coli isolates encoded AMR genes targeted in this study, except OXA-type (Fig. 2d), whilst 40% (2/5) of ESBL producing- Pseudomonas aeruginosa isolates carried a single ESBL gene, CTX-M-type, Fig. 2e.
In general, 73% (24/33) of the ESBL-producing bacteria carried our study’s target AMR genes, mostly CTX-M-type (59%, 17/29), Fig. 2f. Klebsiella pneumoniae isolates harbored the majority of the study ESBL genes identified (76.9%, 20/26), and none of our target ESBL gene was detected in ESBL-producing Acinetobacter baumannii, Fig. 2f.
Distribution Of Resistance Genes Among Mdr Phenotypes Of Esbl-producing Gnb
Isolates resistant to three or more antibiotic classes were considered multidrug-resistant organisms (MDRs) [23]. Eighty-three per cent of GNB harbouring TEM-type (10/12) and SHV-type (100%, 7/7) β-lactamases showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate but most of them remained susceptible to tazobactam (60%, 6/10), Table 3. One of TEM-type β-lactamases (8.3%, 1/12) from E. cloacae complex isolate (410P/NP) seemed to efficiently hydrolyze aztreonam (ATM) than cefotaxime (CTX) or ceftazidime (CAZ) Table 3.
In this study, SHV-type genes carrying ESBL producers showed resistance to both CTX and CAZ (K. pneumoniae isolate, 3OP), CAZ (E. coli, 40BD) or CTX (E. cloacae complex (50OP) and K. pneumoniae (36OP and 44 NP). About 13% (3/24) of bacterial isolates encoding CTX-M-type β-lactamases did not display the typical cefotaxime/ceftriaxone (CTX/CRO) resistance phenotype of the early CTX-M variants. About 42% (5/12) of ESBL-producing GNB with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ), Table 3.
The OXA-1 β-lactamases detected were resistant to third (cefotaxime, CTX; ceftazidime, CAZ; ceftriaxone, CRO) fourth-generation cephalosporins (cefepime, FEP) and monobactam (aztreonam, ATM). One of OXA-type b-lactamases isolated from E. cloacae complex isolates (55OP) showed carbapenemases activity, Table 3.
Table 3
Distribution of resistance genes among MDR phenotypes of ESBL-producing GNB
Bacterial type
|
Isolate ID
|
MDR phenotype
|
ESBL genotype
|
Klebsiella pneumoniae
|
3OP
|
AMC/SAM/CTX/CAZ/CRO/ATM/CIP/COL
|
SHV
|
43TA
|
SAM/CTX/CRO/ATM/SXT
|
CTX-M
|
39OP
|
CTX/CRO/ATM/GEN/SXT/COL
|
CTX-M
|
51BD
|
SAM/CTX/CAZ/CRO/ATM/GEN/SXT
|
CTX-M
|
45OP
|
SAM/CTX/CRO/ATM/GEN/CIP/SXT/COL
|
CTX-M
|
18BD
|
SAM/CTX/CAZ/CRO/FEP/ATM/GEN/SXT
|
CTX-M
|
102TA
|
AMC/SAM/CTX/CAZ/CRO/ATM/GEN/CIP/SXT
|
CTX-M
|
48NP
|
SAM/CTX/CAZ/CRO/ATM/GEN/CIP/SXT/COL
|
CTX-M
|
36OP
|
SAM/CTX/CRO/ATM/GEN/SXT
|
CTX-M + SHV
|
44NP
|
SAM/CTX/CRO/ATM/GEN/CIP/SXT
|
CTX-M + SHV
|
51OP
|
CTX/CRO/ATM/GEN/SXT
|
CTX-M + TEM
|
18OP
|
AMC/SAM/CTX/CRO/ATM/GEN/SXT
|
CTX-M + TEM
|
37OP
|
SAM/CTX/CRO/ATM/GEN/CIP/SXT/COL
|
CTX-M + TEM
|
75BD
|
AMC/SAM/CTX/CAZ/CRO/FEP/ATM/GEN/SXT
|
CTX-M + TEM
|
43OP
|
CTX/CRO/ATM/GEN/SXT
|
CTX-M + TEM, OXA
|
E. cloacae complex
|
35OP
|
AMC/CTX/CRO/ATM/GEN/SXT
|
CTX-M + SHV
|
37NP
|
AMC/CTX/CRO/ATM/GEN/SXT
|
CTX-M + TEM
|
40OP
|
AMC/CTX/CRO/ATM/GEN/CIP/SXT
|
CTX-M + TEM
|
420P
|
AMC/CTX/CAZ/CRO/ATM/GEN/SXT
|
CTX-M + TEM
|
500P
|
AMC/CTX/CRO/ATM/GEN/SXT
|
TEM + SHV
|
410P/NP
|
AMC/TZP/CRO/ATM/GEN/SXT
|
CTX-M + TEM + SHV
|
550P
|
AMC/TZP/CTX/CAZ/CRO/FEP/ATM/MEM/GEN/CIP/SXT
|
CTX-M + OXA
|
Enterobacter cloacae
|
85TA
|
AMC/CTX/CAZ/CRO/ATM
|
TEM
|
31OP
|
AMC/CTX/CAZ/CRO/ATM/GEN/SXT
|
ND
|
Pseudomonas aeruginosa
|
3NP
|
CTX/CRO/ATM/GEN/SXT
|
CTX-M
|
5NP
|
TZP/CTX/CAZ/FEP
|
CTX-M
|
Escherichia coli
|
43NP
|
SAM/CTX/CRO/GEN/CIP/SXT/COL
|
CTX-M
|
40BD
|
AMC/SAM/TZP/CAZ/CRO/FEP/GEN/CIP/SXT
|
CTX-M + TEM + SHV
|
40NP
|
SAM/CTX/CRO/GEN/CIP/SXT
|
ND
|
Acinetobacter baumannii
|
21TA
|
TZP/CTX/CAZ/CRO/FEP/MEM/CIP/SXT
|
ND
|
36BD
|
SAM/TZP/CTX/CAZ/CRO/FEP/GEN/CIP/SXT
|
ND
|
94TA
|
TZP/CTX/CAZ/CRO/FEP/GEN/CIP/SXT
|
ND
|
112TA
|
CTX/CRO/FEP/CIP/SXT
|
ND
|
AMC amoxicillin/clavulanate, SAM ampicillin/sulbactam, TZP piperacillin/tazobactam, CTX cefotaxime, CAZ ceftazidime, CRO ceftriaxone, FEP cefepime, ATM aztreonam, MEM meropenem, COL colistin, GEN gentamicin; CIP ciprofloxacin, SXT trimethoprim/sulfamethoxazole, ESBLs extended spectrum β- lactamases, TEM temoneira -type β-lactamases, CTX-MCefotaxime-hydrolysing b-lactamase isolated in Munich-type β-lactamases, SHV sulfhydryl variable-type β-lactamases, OXA-1 Oxacillinases -type β-lactamases 1, ND Not Detected
Factors Associated With Esbl-producing Gnb Infections Among Covid-19 Patients Admitted To Knh-idu
Multivariable analysis established that severely ill COVID-19 patients with comorbidities were about ten (10) times more likely to have an infection caused by ESB-producing GNB (aOR = 9.86, 95%CI: 1.30–74.63, p = 0.003). Male gender was also a risk factor for infection with ESBL-producing GNB, although there was no independent association (cOR = 9.97(2.32–42.85), p = 0.002), Table 4.
Table 4
Factors associated with ESBL-producing GNB infections among COVID-19 patients admitted to KNH-IDU
Factors
|
ESBL producer
|
cOR(95%CI)
|
P-value
|
aOR(95%CI)
|
P-value
|
Yes n (%)
|
No n (%)
|
Age (years)
|
<=24
|
2(6.1)
|
3(18.8)
|
3.90(0.49–30.76)
|
0.196
|
13.95(0.74–23.11)
|
0.078
|
25–44
|
9(27.3)
|
3(18.8)
|
0.87(0.16–4.58)
|
0.866
|
2.02(0.21–19.44)
|
0.542
|
45–59
|
9(27.3)
|
5(31.3)
|
1.44(0.32–6.49)
|
0.632
|
3.67(0.40–33.96)
|
0.252
|
>=60
|
13(39.4)
|
5(31.3)
|
Ref
|
|
Ref
|
|
Gender
|
Male
|
23(69.7)
|
3(18.8)
|
9.97(2.32–42.85)
|
0.002
|
3.38(0.59–19.43)
|
0.172
|
Female
|
10(30.3)
|
13(81.3)
|
Ref
|
|
Ref
|
|
Marital status
|
Single
|
7(21.2)
|
6(37.5)
|
0.45(0.12–1.67)
|
0.231
|
|
|
Married
|
26(78.8)
|
10(62.5)
|
Ref
|
|
|
|
Presence of comorbidity
|
Yes
|
30(90.9)
|
8(50.0)
|
10.0(2.15–46.61)
|
0.003
|
9.86(1.30–74.63)
|
0.027
|
No
|
3(9.1)
|
8(50)
|
|
|
Ref
|
|
SARS-CoV-2 Vaccination status
|
Yes
|
8(24.2)
|
3(18.8)
|
1.39(0.31–6.13)
|
0.483
|
|
|
No
|
25(75.8)
|
13(81.3)
|
Ref
|
|
|
|
Hospitalization outcome
|
Alive
|
27(81.8)
|
11(68.8)
|
2.05(0.52–8.12)
|
0.466
|
|
|
Died
|
6(18.2)
|
5(31.3)
|
Ref
|
|
|
|
Length of hospital stay (Days)
|
Short stay (0–5)
|
9(27.3)
|
2(12.5)
|
Ref
|
|
Ref
|
|
Medium stay (6–10)
|
17(51.5)
|
8(50)
|
0.26(0.04–1.70)
|
0.159
|
0.39(0.04–4.02)
|
0.425
|
Long stay (> 10)
|
7(21.2)
|
6(37.5)
|
0.55(0.14–2.18)
|
0.393
|
0.43(0.06–2.96)
|
0.39
|
cOR crude odds ratio, aOR adjusted odds ratio, ESBLs extended spectrum beta-lactamases, Ref Reference, SARS-CoV-2 severe acute respiratory syndrome coronavirus 2, CI confidence interval.