The extent of carbapenem-resistant encoding genes in Klebsiella pneumoniae from COVID-19 and non-COVID-19 patients in a tertiary care center, Saudi Arabia

Abstract

Rapid dissemination of Klebsiella pneumoniae carbapenemase (KPC) is a leading cause of treatment failure, significantly increasing morbidity and mortality rates among inpatients, particularly in the intensive care unit (ICU). This study aimed to detect the occurrence of carbapenemase- and carbapenem-resistant-encoding genes in K. pneumoniae isolates from COVID-19 positive and negative patients, and to assess their impact on patient outcomes. A prospective analysis was conducted at a tertiary care hospital in Saudi Arabia, collecting 97 carbapenem-resistant K. pneumoniae (CRKP) isolates from patients with COVID-19 during 2020-2021. Isolates were obtained from various clinical specimens. Antimicrobial susceptibility assays were performed using the Automated Vitek-2 system, and data were analyzed using IBM SPSS Statistics. The predominant carbapenemases identified were Oxacillinase-48 (OXA-48), followed by KPC and New Delhi metallo-β-lactamase (NDM), with Imipenemase (IMP) and Verona integron-encoded metallo-β-lactamase (VIM) being the least prevalent. COVID-19 did not significantly affect the distribution of these genes (P>0.05); however, COVID-19 status and age over 60 years significantly impacted the outcomes of CRKP patients. Other factors such as gender, total ICU or ward stay, and comorbidities did not significantly affect CRKP infection outcomes. The most common carbapenem-resistant genes identified were blaKPC, blaNDM, and blaOXA-48; however, they were not significantly associated with increased mortality.

Klebsiella pneumoniae; Carbapenem; Antibiotic resistance; Coronavirus; Saudi Arabia

Introduction

The incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP), also known as extended-spectrum beta-lactamase-producing K. pneumoniae (ESBL-KP), has been universally described (¹,²). CRKP appears to be a significant agent of severe disease and has increased continuously, leading to a substantial hazard for healthcare workers. They are commonly multi-drug resistant and often compromise treatment outcomes (³). There is an elevated incidence of carbapenemase- and carbapenem-resistant encoding genes among Enterobacteriaceae that are resistant to third-generation cephalosporins in many parts of the world. This situation limits treatment choices. CRKP infections cause high morbidity and mortality rates, particularly in developing countries. Similar to other regions, an increase in CRKP incidence has been observed in Saudi Arabia (⁴). Every year, many visitors and workers come to Saudi Arabia with OXA-48 and from countries with rampant New Delhi metallo-β-lactamase (NDM), such as Turkey, India, and Pakistan (⁵). In Iran, the proportion was estimated to be 11.3% (95% confidence interval (CI): 0.084-0.15) (⁶), which is due to several resistance-mediated genes that facilitate antimicrobial drug resistance in K. pneumoniae (⁷). The proportion and categories of CRKP isolates vary significantly in several Mediterranean countries. This region is an area of dissemination for many multi-resistant pathogens caused by many geographic and epidemiological factors, especially the international crossing of patients, many of whom come from endemic zones (⁸).

According to the Ambler classification, beta-lactamases are organized into four molecular categories (A, B, C, and D) based on their amino acid sequences (⁹). Some of the most common carbapenemases include Klebsiella pneumoniae carbapenemase (KPC) (class A), NDM, Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM) (Class B), and Oxacillinase (OXA) (class D). They are plasmid-coded and are transferred primarily by conjugation from one bacterium to another (¹⁰). Enzymes are arranged based on their ability to hydrolyze specific β-lactam classes. Inactivation properties of β-lactamase inhibitors include clavulanic acid, sulbactam, and tazobactam. Each functional group is explained by Bush and Jacoby (¹¹).

Multidrug-resistant K. pneumoniae isolates containing carbapenemase- and carbapenem-resistant genes, blaOXA-48, blaNDM, and colistin resistance, are believed to have emerged in Saudi Arabia (⁵). The main type of carbapenemase was OXA-48 (81.5%, n=44), and it seems to have reached an endemic level. New Delhi metallo-β-lactamases (NDM) was the second most frequent carbapenemase in 7.4% (n=4) of the isolates, although Verona integron-encoded metallo-β-lactamases (VIM) was described in one isolate (⁵) in 2018. Recently, we noted an increase in K. pneumoniae, which is a threat to ICU patients and has been linked to nearly half of ICU deaths (¹²). Tigecycline alone or with colistin in a high-dose course of therapy was found to be a promising treatment for CRKP infections (¹³). Demographic and clinical aspects have been found to be associated with the expansion of CRKP (¹⁴). The need to focus on CRKP infection in COVID-19 patients has increased.

Patient outcomes are negatively affected by the increasing prevalence of CRKP, particularly during the COVID-19 pandemic. The risk of hospital-acquired infections, mainly among those caused by CRKP, is worsened in COVID-19 patients due to severe respiratory issues, lengthy hospitalization, mechanical ventilation, and the use of broad-spectrum antibiotics (¹⁵,¹⁶). The immunocompromised state induced by COVID-19 further increases the susceptibility to secondary infections, making the presence of CRKP a serious concern. Studies have indicated that co-infection with multidrug-resistant organisms, including CRKP, is related to higher mortality rates in COVID-19 patients (¹⁷,¹⁸). Furthermore, the healthcare burden associated with CRKP infections in nurses during the pandemic can stretch the already inadequate resources, complicating the management of both COVID-19 and resistant infections (¹⁹). Therefore, understanding the prevalence and effect of CRKP in COVID-19 patients is critical for developing effective treatment and infection control actions in healthcare settings.

The current study aimed to detect the rate of carbapenemase- and carbapenem-resistant-encoding genes in CRKP isolates among COVID-19 positive and negative patients and their effect on patient outcomes in the southwestern region of Saudi Arabia.

Material and Methods

Study design

The present study was a cross-sectional investigation conducted between January 2020 and December 2021 in the Asir Central Hospital (ACH), Saudi Arabia.

Criteria for inclusion and exclusion of K. pneumoniae

Isolates of K. pneumoniae that displayed reduced sensitivity to carbapenems from all patients (n=97) were included. K. pneumoniae isolates found sensitive to carbapenems were eliminated. Duplicate isolates from similar patients were also omitted, except when they were isolated from different specimens with dissimilar clinical or susceptibility patterns. Patients with COVID-19 who had a positive PCR test and those with symptoms associated with the virus, as determined by laboratory testing, met the study's inclusion criteria. Patients with respiratory symptoms and negative PCR findings were excluded, as were those with other bacterial or viral infections that would make the identification of COVID-19 more difficult.

Diagnostic testing in COVID-19

The confirmation of COVID-19 was done following standard diagnostic testing (²⁰). Nasopharyngeal samples were collected with swabs and analyzed for SARS-CoV-2 nucleic acid using the commercial real-time PCR assay kit available at ACH.

Isolation and identification of K. pneumoniae

A collection of CRKP isolates (n=97) from COVID-19-positive patients exhibited reduced sensitivity to carbapenems. Isolates were initially identified in a microbiology laboratory using selected bench phenotypic tests (²⁰) and then confirmed using an automated Vitek-2 identification system (BioMerieux, France) and Vitek card GN following the manufacturer's instructions. K. pneumoniae ATCC 19593, NCTC 13438 (KPC), NCTC 13443 (NDM), NCTC 13440 (VIM), and NCTC 13442 (OXA-48) were used as quality control strains.

Antibiotic susceptibility assay

Antimicrobial susceptibility testing was performed using the Vitek-2 system (Vitek card AST-N92) according to the manufacturer's instructions. The antimicrobial agents tested included ampicillin, piperacillin-tazobactam, amoxicillin-clavulanate, ceftazidime, imipenem, cefepime, meropenem, amikacin, gentamicin, ciprofloxacin, tigecycline, and trimethoprim-sulfamethoxazole.

Molecular analysis of carbapenem-resistant encoding genes

The carbapenemase genes blaIMP, blaKPC, blaNDM, blaOXA-48, and blaVIM of all K. pneumoniae isolates were screened by multiplex polymerase chain reaction following the protocol described by Zarakolu et al. (²¹) using the primers listed in Table 1 (²⁰,²²,²³) from Macrogen Inc. (South Korea).

Table 1
Primer sets used to detect Klebsiella pneumoniae carbapenem-resistant encoding genes.

Target	Primer name	Primer sequence (5′ to 3′)	Reference
blaIMP	IMP-F	5′-GGAATAGAGTGGCTTAATTC-3′	(20)
	IMP-R	5′-GCCAAGCTTCTATATTTGCG-3′
blaKPC	KPC-F	5′-TCGCTAAACTCGAACAGG-3′	(22)
	KPC-R	5′-TTACTGCCCGTTGACGCCCAATCC-3′
blaNDM	NDM-F	5′-GGGCAGTCGCTTCCAACGGT-3′	(23)
	NDM-R	5′-GTAGTGCTCAGTGTCGGC-3′
blaVIM	VIM-F	5′-GTGTTTGGTCGCATATCGC-3′	(20)
	VIM-R	5′-CGCAGCACCAGGATAGAAG-3′

A loopful of a fresh colony of CRKP was placed in a microcentrifuge tube that contained 300 µL sterile distilled water (HiMedia, India). The suspension was mixed well and heated for 10 min at 96°C. The suspension was then placed on an ice tray for 2 min. The suspension was next centrifuged for 5 min at 13,000 g at 25°C, and two microliters of the supernatant were used for the PCR reaction.

Multiplex PCR was performed for all CRKP isolates following the methods of Zarakolu et al. (²¹). Concisely, a 25 µL PCR reaction having 12.5 µL of Taq PCR master mix (Qiagen, Germany), 0.5 µL sterile RNase-free water, 2 µM of each primer (1 µL of 50 µM), and 2 µL of DNA template was applied in the PCR amplification (total of 23 µL). The amplification stages comprised a 5-min denaturation at 95°C, followed by 36 cycles of 94°C for 45 s, 53°C for 45 s, 72°C for 1 min, and a final extension at 72°C for 6 min.

PCR products were tracked on a 1.5% agarose gel (Promega, USA) containing 0.5 µg/µL ethidium bromide. The gel was subjected to electrophoresis in 1x tris-borate-EDTA (TBE) buffer at 100 V for 55 min using an electrophoresis system (Bio-Rad, USA). A 50-bp ladder was used as the molecular size marker. The DNA bands were visualized using a Syngene Gel Detection and Documentation System (Syngene, UK).

Statistical analysis

Descriptive statistics were used to summarize the epidemiological characteristics of CRKP strains. Analyses were performed using IBM SPSS Statistics (version 21, USA). Student's t-test was used to compare continuous variables, and Fisher's exact test or chi-squared test was used to compare categorical variables. Binary logistic regression analysis was performed to identify probable risk factors (demographic, epidemiological, and clinical) for death among ESBL-KP patients in southern Saudi Arabia. P-values were obtained using the 2-tailed method, and statistical significance was set at P<0.05.

Results

Distribution of resistant K. pneumoniae strains according to demographic and clinical data from the COVID-19 positive patients

The descriptive analysis of CRKP according to COVID-19 positive and COVID-19 negative subjects and the corresponding demographic and clinical data are presented in Table 2.

Table 2
Distribution of clinical characteristics and outcomes among COVID-19 negative and positive patients.

Factor	COVID-19 Negative		COVID-19 Positive
	Count	%	Count	%
Gender
Female	19	24	12	15
Male	21	27	27	34
Age group (years)
<30	4	5	1	1
>60	19	24	24	30
31 to 60	17	22	14	18
Specimen
Abdominal drain	5	6	0	0
Blood	11	14	13	16
CSF	2	3	0	0
Peritoneal fluid	1	1	0	0
Sputum	14	18	23	29
Urine	2	3	2	3
Wound	5	6	1	1
Comorbidity
AF, COPD	1	1	0	0
ALS	0	0	0	0
CKD	1	1	0	0
DM	3	4	10	13
DM, HTN	7	9	7	9
DM, HTN, IHD	2	3	1	1
ESRD	1	1	0	0
ESRD, post-COVID-19	1	1	0	0
HCC, AF, Old CVA	1	1	0	0
HTN	6	8	5	6
HTN, IHD	0	0	2	3
Liver transplant	0	0	1	1
Malonic acidemia	0	0	1	1
Old CVA	0	0	1	1
RA, Hx of COVID-19	1	1	0	0
No comorbidity	16	20	11	14
Total ICU stay (days)
0	7	9	11	14
1 to 10	10	13	20	25
11 to 20	10	13	7	9
21 to 30	4	5	1	1
>30	9	11	0	0
Bounce Back
No	33	42	36	46
Yes	7	9	3	4
Outcome
Cured	26	33	10	13
Dead	14	18	29	37
IMP
Negative	39	49	39	49
Positive	1	1	0	0
VIM
Negative	38	48	39	49
Positive	2	3	0	0
NDM
Negative	27	34	20	25
Positive	13	16	19	24
KPC
Negative	26	33	17	22
Positive	14	18	22	28
OXA-48
Negative	16	20	28	35
Positive	24	30	11	14

• CSF: cerebrospinal fluid AF: atrial fibrillation; COPD: chronic obstructive pulmonary disease; ALS: amyotrophic lateral sclerosis; CKD: chronic kidney disease; DM: diabetes mellitus; HTN: hypertension; IHD: ischemic heart disease; ESRD: end-stage renal disease; HCC: hepatocellular carcinoma; CVA: cerebrovascular accident (stroke); RA: rheumatoid arthritis.

There was a higher percentage of males in both groups, with 34% of COVID-19 positive patients being male versus 27% in the negative group. Also, 30% of COVID-19 positive patients were over 60 years old, compared to 24% in the negative group, while the younger age group (<30 years) had fewer cases in both groups. Sputum samples were more often obtained from COVID-19 positive patients (29%) than negative patients (18%), suggesting a correlation with respiratory involvement. Notably, diabetes mellitus (DM) was more prevalent among COVID-19 positive patients (13%) compared to 4% in the negative group, as well as similar trends in other comorbidities like hypertension. Furthermore, 18% of COVID-19 positive patients had ICU stays exceeding 21 days, compared to only 3% in the negative group, indicating more severe illness. The cure rate was significantly lower for COVID-19 positive patients than for negative patients (13 vs 33%), with mortality rates higher in the positive group (37 vs 18%).

Distribution of carbapenemase-encoding genes

Table 2 summarizes the distribution of carbapenemase-encoding genes among COVID-19 patients, demonstrating that 49% of both negative and positive groups tested negative for IMP, with no positive cases in the latter. A comparable trend was noted for VIM, for which 48% of negative and 49% of positive patients tested negative, once more with no positives found in the COVID-19 positive group. For NDM, 34% of COVID-19 negative patients were negative, while 25% of positives tested negative; however, 16% of the negative group and 24% of the positive group were positive for NDM, indicating a higher prevalence among COVID-19 positive patients. Regarding KPC, 33% of COVID-19 negative patients were negative, compared to 22% of positives, with 18% of negatives and 28% of positives testing positive, highlighting a stronger association with COVID-19. Lastly, for OXA48, 20% of COVID-19 negative patients tested negative, while 35% of positives were negative; in contrast, 30% of negatives tested positive vs only 14% of positives.

Effect of dominant CRKP on patient outcome

The effect of CRKP on the outcomes of 97 patients is shown in Figure 1. Mortality was linked to higher levels of carbapenemases, namely blaKPC, blaNDM, and blaOXA48. The effects of COVID-19, sex, age group, and ICU stay on patient mortality in this study are shown in Figure 2. Comparably, mortality was associated with COVID-19 infection and age >60 years (Table 2; Figure 2).

Figure 1
Effect of carbapenemase-encoding genes on patient mortality (%). Data are reported as means and SE. Chi-squared test. NDM, the odds ratio (Exp(B)=0.884) suggested a non-significant trend towards lower odds of a favorable outcome. KPC showed an Exp(B) of 0.748 (P=0.524), indicating no significant effect on the outcome as well, with a 95%CI of 0.307 to 1.827, and OXA-48 had an Exp(B) of 1.243 (P=0.633), revealing no important association with outcomes, supported by a 95%CI of 0.509 to 3.031.

Figure 2
Effect of COVID-19, gender, age group, and intensive care unit (ICU) stay on patient mortality (%). Data are reported as means and SE. Chi-squared test: positive COVID-19 (P=0.001), age >60 (P=0.004), gender (P=0.387), total ICU stay (P=0.380).

Mortality predictors among CRKP patients

Table 3 shows the outcome predictors (cured or deceased) among CRKP patients with COVID-19 in southern Saudi Arabia, based on binary logistic regression analysis. The investigation showed that the presence of IMP did not significantly influence the outcome (P=1.000). VIM also showed no significant link (P=0.999). For NDM, the odds ratio (Exp(B)=0.884) suggested a non-significant trend towards lower odds of a favorable outcome, with a 95% confidence interval (95%CI) ranging from 0.358 to 2.181. KPC showed an Exp(B) of 0.748 (P=0.524), indicating no significant effect on the outcome as well, with a 95%CI of 0.307 to 1.827. Lastly, OXA-48 had an Exp(B) of 1.243 (P=0.633), revealing no important association with outcomes, supported by a 95%CI of 0.509 to 3.031. These findings suggested that none of the tested carbapenemase-encoding genes significantly predicted patient outcomes in this cohort.

Table 3
Predictors of outcome (cured, died) among extended-spectrum carbapenem-resistant Klebsiella pneumoniae COVID-19 patients* in southern Saudi Arabia according to binary logistic regression analysis.

Factor	P	Exp(B)	95%CI for EXP(B)
			Lower	Upper
COVID-19
Positive vs Negative	0.001	0.186	0.070	0.489
Constant	0.004	2.900
Gender
Male vs female	0.387	0.670	0.270	1.661
Constant	0.250	1.400
Age group (years)
Overall	0.014
31 to 60	0.845	1.212	0.175	8.389
>60	0.004	4.196	1.571	11.205
Constant (<30)	0.111	0.550
Specimen
Overall	0.495
Abdominal drain	0.999	0.000	0.000
Blood	0.051	10.000	0.994	100.612
CSF	0.999	b	0.000
Peritoneal fluid	1.000	b	0.000
Sputum	0.082	7.333	0.777	69.236
Urine	0.748	1.667	0.074	37.728
Constant (wound)	0.142	0.200
Total ICU stay (days)
Overall	0.380
>30	0.153	0.389	0.107	1.420
1 to 10	0.999	0.000	0.000
11 to 20	0.089	0.111	0.009	1.395
21 to 30	0.730	0.750	0.146	3.841
Constant (0 day)	0.057	3.000
Total ward stay (days)
Overall	0.039
>30	1.000	1.000	0.000
1 to 10	0.999	b	0.000
11 to 20	0.999	b	0.000
21 to 30	0.999	b	0.000
Constant (0 day)	0.999	0.000
Comorbidity
Overall	0.933
AF, COPD	0.999	0.000	0.000
CKD	0.999	0.000	0.000
DM	1.000	0.000	0.000
DM, HTN	1.000	0.000	0.000
DM, HTN, IHD	0.999	0.000	0.000
ESRD	0.999	0.000	0.000
ESRD, post covid	1.000	1.000	0.000
HCC, AF, old CVA	1.000	1.000	0.000
HTN	1.000	0.000	0.000
HTN, IHD	1.000	1.000	0.000
Liver transplant	1.000	1.000	0.000
Malonic acidemia	1.000	1.000	0.000
No comorbidities	1.000	0.000	0.000
Old CVA	1.000	1.000	0.000
Constant (RA, Hx of Covid)	1.000	b
Bounce Back
Positive vs Negative	0.101	0.257	0.051	1.300
Constant	0.080	4.000
IMP
Positive vs Negative	1.000	0.000	0.000
Constant	1.000	b
VIM
Positive vs Negative	0.999	b	0.000
Constant	0.999	0.000
NDM
Positive vs Negative	0.789	0.884	0.358	2.181
Constant	0.481	1.286
KPC
Positive vs Negative	0.524	0.748	0.307	1.827
Constant	0.320	1.400
OXA-48
Positive vs Negative	0.633	1.243	0.509	3.031
Constant	0.866	1.059

• *The transferred cases were omitted in this analysis to allow binary regression; b: omitted count as the number was large. CSF: cerebrospinal fluid; AF: atrial fibrillation; COPD: chronic obstructive pulmonary disease; ALS: amyotrophic lateral sclerosis; CKD: chronic kidney disease; DM: diabetes mellitus; HTN: hypertension; IHD: ischemic heart disease; ESRD: end-stage renal disease; HCC: hepatocellular carcinoma; CVA: cerebrovascular accident (stroke); RA: rheumatoid arthritis.

Discussion

Worldwide, there is an increasing occurrence of carbapenemase- and carbapenem-resistant genes in K. pneumoniae (²⁴). A similar trend has been observed in regions in the Kingdom of Saudi Arabia, where multidrug-resistant K. pneumoniae isolates with carbapenemases have been reported (⁵,²⁰- ²²). This causes significant morbidity and mortality, especially in developing countries (²⁵). It appears primarily in gram-negative bacteria such as K. pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and other members of clinical Enterobacteriaceae, and can be inherent or predominantly facilitated by acquired carbapenemase-encoding genes (²⁶).

The findings of a previous study in hospitals in a Southern Saudi province in 2015 indicate that the isolation of CRKP is related to old age, similar to our current findings. This result agrees with that of Kofteridis et al. (²⁷), who showed that older age is an important risk factor related to CRKP isolation. Notably, our results showed that ICU patients are likely to be susceptible to CRKP infection. Earlier reports have also stated that ICU and pre-ICU admissions are linked to CRKP colonization and infection. In the present study, more than one-third of K. pneumoniae isolates (42.6%, n=23) were isolated from ICU patients. The incidence of CRKP in a meta-analysis was found to be 43.5% (95%CI: 39.3-47.9%) in the K. pneumoniae isolates recovered from patients. Among the genes encoding ESBLs during 2000-2009, SHV, CTX-M, and TEM were observed at frequencies of 23.3, 15.2, and 12.3%, respectively. The frequencies of SHV, CTX-M, TEM, and VEB were 24.0, 28.1, 25.2, and 8.3%, respectively, throughout the period 2010-2018 (¹).

Indications from surveillance investigations have emphasized a rise in mortality in patients with CRKP infection linked to their carbapenem-susceptible (CSKP) matching part; nonetheless, the particular causes of this mortality are hitherto unclear (²⁸). Several independent risk factors for mortality among patients with CRKP infections have been documented (²⁹). We determined that increased mortality was associated with COVID-19 co-infection in patients aged >60 years. Older age has been increasingly reported in the literature as a risk factor for morbidity and mortality from CRKP infection. Risk factors such as preceding ICU stay, prior surgical procedure, and renal disease were associated with the development of CRKP infection/colonization (²⁷). Our findings agreed on the effect of older age, but ICU stay did not have a significant effect on the outcome of CRKP patients.

Bacteremia with CRKP was found to be an independent risk factor for death, supporting strict adherence to cohort and isolation procedures (³⁰). Bacteria in the lung infection group were mostly gram-negative bacteria (22, 68.8%), especially K. pneumoniae, 13 (40.6%) were gram-positive bacteria and fungi, mostly Staphylococcus aureus, and 11 (34.4%) were primarily Candida albicans. Fourteen patients (43.8%) were infected with two or more agents (³¹). Early antibiotic contact was found to be a possible risk factor for CRKP. Nonetheless, mortality among patients with K. pneumoniae bacteremia was found to be associated with severe comorbidities, but not with carbapenem resistance (³²). Our study indicated that comorbidities, mainly diabetes mellitus and hypertension, were elevated, but not significantly associated with mortality.

The findings showed that 49% of both negative and positive COVID-19 patients groups tested negative for IMP, and a similar pattern was observed for VIM. While NDM exhibited a higher prevalence in COVID-19 positive patients (24% positive) compared to negatives (16%), the presence of these genes did not significantly influence patient outcomes, as indicated in Table 3. The odds ratios for NDM (Exp(B)=0.884), KPC (Exp(B)=0.748), and OXA-48 (Exp(B)=1.243) suggested no significant associations with mortality. In the Riyadh region, only two isolates from a single patient were resistant to carbapenems. CTX-M and SHV genes were identified in every isolate, with CTX-M-15 and SHV-1 being the most prevalent among these ESBLs. TEM-1 was detected in all isolates (isolate 3). Remarkably, OXA-48 was retrieved from all isolates. The OXA-D gene was located in three of the 23 isolates. KPC, NDM, OXA-A, OXA-B, OXA-C, VIM, and IMP genes were nonexistent in all isolates (³³). According to a previous finding (³⁴), blaNDM is the second most prevalent gene after blaKPC. The number of multidrug-resistant K. pneumoniae isolates with blaOXA-48, blaNDM, and colistin resistance has been increasing in Saudi Arabia in recent years (³²). Carbapenems can resist many β-lactamase enzymes and are usually scheduled as the last treatment option for severe infections caused by ESBL-producing Enterobacteriaceae.

Conclusion

The present study indicated that in patients suffering from CRKP in association with COVID-19, older age was a risk factor for high mortality. Overall, the findings suggested that certain carbapenemase genes, particularly NDM and KPC, may be more prevalent in COVID-19 patients, warranting further investigation into their clinical implications.

• Funding
  The authors extend their appreciation to the Deanship of Scientific Research at King Khalid University for funding this work through the General Research Project under the grant number GRP/145/44.

References

• ¹ Beigverdi R, Jabalameli L, Jabalameli F, Emaneini M. Prevalence of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae: first systematic review and meta-analysis from Iran. J Glob Antimicrob Resist. 2019;18:12-21, doi: 10.1016/j.jgar.2019.01.020.
  » https://doi.org/10.1016/j.jgar.2019.01.020
• ² Yaita K, Komatsu M, Oshiro Y, Yamaguchi Y. Postoperative meningitis and epidural abscess due to extended-spectrum β-lactamase-producing Klebsiella pneumoniae: a case report and a review of the literature. Intern Med. 2012;51(18):2645-2648, doi: 10.2169/internalmedicine.51.8068.
  » https://doi.org/10.2169/internalmedicine.51.8068
• ³ Malloy AM, Campos JM. Extended-spectrum beta-lactamases: a brief clinical update. Pediatr Infect Dis J. 2011;30(12):1092-1093, doi: 10.1097/INF.0b013e31823c0e9d.
  » https://doi.org/10.1097/INF.0b013e31823c0e9d
• ⁴ Alotaibi F. Carbapenem-resistant enterobacteriaceae: an update narrative review from Saudi Arabia. J Infect Public Health. 2019;12(4):465-471, doi: 10.1016/j.jiph.2019.03.024.
  » https://doi.org/10.1016/j.jiph.2019.03.024
• ⁵ Al-Zahrani IA, Alsiri BA. The emergence of carbapenem-resistant Klebsiella pneumoniae isolates producing OXA-48 and NDM in the Southern (Asir) province, Saudi Arabia. Saudi Med J. 2018;39(1):23-30, doi: 10.15537/smj.2018.1.21094.
  » https://doi.org/10.15537/smj.2018.1.21094
• ⁶ Vaez H, Sahebkar A, Khademi F. Carbapenem-resistant Klebsiella pneumoniae in Iran: a systematic review and meta-analysis. J Chemother. 2019;31(1):1-8, doi: 10.1080/1120009X.2018.1533266.
  » https://doi.org/10.1080/1120009X.2018.1533266
• ⁷ Effah CY, Sun T, Liu S, Wu Y. Klebsiella pneumoniae: an increasing threat to public health. Annals of Clinical Microbiology and Antimicrobials. 2020;19(1):1, doi: 10.1186/s12941-019-0343-8.
  » https://doi.org/10.1186/s12941-019-0343-8
• ⁸ Girmenia C, Serrao A, Canichella M. Epidemiology of Carbapenem Resistant Klebsiella pneumoniae infections in mediterranean countries. Mediterr J Hematol Infect Dis 2016;8(1):e2016032, doi: 10.4084/mjhid.2016.032.
  » https://doi.org/10.4084/mjhid.2016.032
• ⁹ Sawa T, Kooguchi K, Moriyama K. Molecular diversity of extended-spectrum beta-lactamases and carbapenemases, and antimicrobial resistance. J Intensive Care. 2020;8:13, doi: 10.1186/s40560-020-0429-6.
  » https://doi.org/10.1186/s40560-020-0429-6
• ¹⁰ Queenan AM, Bush K. Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev 2007;20(3):440-458, doi: 10.1128/CMR.00001-07.
  » https://doi.org/10.1128/CMR.00001-07
• ¹¹ Bush K, Jacoby GA. Updated functional classification of beta-lactamases. Antimicrobial agents and chemotherapy. Antimicrob Agents Chemother. 2010;54(3):969-976, doi: 10.1128/AAC.01009-09.
  » https://doi.org/10.1128/AAC.01009-09
• ¹² Larcher R, Laffont-Lozes P, Roger C, et al. Last resort beta-lactam antibiotics for treatment of New-Delhi metallo-beta-lactamase producing Enterobacterales and other difficult-to-treat resistance in gram-negative bacteria: a real-life study. Front Cell Infect Microbiol. 2022;12:1048633, doi: 10.3389/fcimb.2022.1048633.
  » https://doi.org/10.3389/fcimb.2022.1048633
• ¹³ Al Bshabshe A, Al-Hakami A, Alshehri B, et al. Rising Klebsiella pneumoniae infections and its expanding drug resistance in the intensive care unit of a Tertiary Healthcare Hospital, Saudi Arabia. Cureus. 2020;12(8):e10060, doi: 10.7759/cureus.10060.
  » https://doi.org/10.7759/cureus.10060
• ¹⁴ Zhang Y, Guo LY, Song WQ, Wang Y, Dong F, Liu G. Risk factors for carbapenem-resistant K. pneumoniae bloodstream infection and predictors of mortality in Chinese paediatric patients. BMC Infect Dis. 2018;18(1):248, doi: 10.1186/s12879-018-3160-3.
  » https://doi.org/10.1186/s12879-018-3160-3
• ¹⁵ van Duin D, Barlow G, Nathwani D. The impact of the COVID-19 pandemic on antimicrobial resistance: a debate. JAC-Antimicrob Resist. 2020;2, doi: 10.1093/jacamr/dlaa053.
  » https://doi.org/10.1093/jacamr/dlaa053
• ¹⁶ Langford BJ, So M, Raybardhan S, Leung V, Soucy JPR, Westwood D, et al. Antibiotic prescribing in patients with COVID-19: a rapid review and meta-analysis. Clin Microbiol Infect. 2021;27(4):520-531, doi: 10.1016/j.cmi.2020.12.018.
  » https://doi.org/10.1016/j.cmi.2020.12.018
• ¹⁷ Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, et al. Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet 2020;395(10229):1054-1062, doi: 10.1016/S0140-6736(20)30566-3.
  » https://doi.org/10.1016/S0140-6736(20)30566-3
• ¹⁸ Alhazzani W, Møller MH, Arabi YM, Loeb M, Gong MNg, Fan E, et al. Surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease 2019 (COVID-19). Crit Care Med. 2020:48(6):e440-e469, doi: 10.1097/CCM.0000000000004363.
  » https://doi.org/10.1097/CCM.0000000000004363
• ¹⁹ Segala FV, Bavaro DF, Di Gennaro F, Salvati F, Marotta C, Saracino A, et al. Impact of SARS-CoV-2 Epidemic on antimicrobial resistance: A literature review. Viruses 2021; 13(11):2110, doi: 10.3390/v13112110.
  » https://doi.org/10.3390/v13112110
• ²⁰ Al-Abdely H, AlHababi R, Dada HM, Roushdy H, Alanazi MM, Alessa AA, et al. Molecular characterization of carbapenem-resistant Enterobacterales in thirteen tertiary care hospitals in Saudi Arabia. Ann Saudi Med. 2021;41(2):63-70, doi: 10.5144/0256-4947.2021.63.
  » https://doi.org/10.5144/0256-4947.2021.63
• ²¹ Zarakolu P, Eser OK, Aladag E, Al-Zahrani IA, Day KM, Atmaca O, et al. Epidemiology of carbapenem-resistant Klebsiella pneumoniae colonization: a surveillance study at a Turkish university hospital from 2009 to 2013. Diagn Microbiol Infect Dis. 2016;85(4):466-470, doi: 10.1016/j.diagmicrobio.2016.05.012.
  » https://doi.org/10.1016/j.diagmicrobio.2016.05.012
• ²² Al-Tawfiq JA, Rabaan AA, Saunar JV, Bazzi AM. Genotypes and prevalence of carbapenemase-producing Enterobacteriaceae and Pseudomonas aeruginosa in a hospital in Saudi Arabia. Trans R Soc Trop Med Hyg. 2022;116(1):50-53, doi: 10.1093/trstmh/trab055.
  » https://doi.org/10.1093/trstmh/trab055
• ²³ Khan MA, Mohamed AM, Faiz A, Ahmad J. Enterobacterial infection in Saudi Arabia: first record of Klebsiella pneumoniae with triple carbapenemase genes resistance. J Infect Dev Ctries. 2019;13(4):334-341, doi: 10.3855/jidc.11056.
  » https://doi.org/10.3855/jidc.11056
• ²⁴ Shahid M, Ahmad N, Saeed NK, Shadab M, Joji RM, Al-Mahmeed A, et al. Clinical carbapenem-resistant Klebsiella pneumoniae isolates simultaneously harboring bla (NDM-1), bla (OXA) types and qnrS genes from the Kingdom of Bahrain: resistance profile and genetic environment. Front Cell Infect Microbiol. 2022;12:1033305, doi: 10.3389/fcimb.2022.1033305.
  » https://doi.org/10.3389/fcimb.2022.1033305
• ²⁵ Codjoe FS, Donkor ES. Carbapenem resistance: a review. Med Sci (Basel). 2017;6(1):1, doi: 10.3390/medsci6010001.
  » https://doi.org/10.3390/medsci6010001
• ²⁶ Fernández J, Guerra B, Rodicio MR. Resistance to Carbapenems in non-typhoidal Salmonella enterica serovars from humans, animals and food. Vet Sci. 2018;5(2):40, doi: 10.3390/vetsci5020040.
  » https://doi.org/10.3390/vetsci5020040
• ²⁷ Kofteridis DP, Valachis A, Dimopoulou D, Maraki S, Christidou A, Mantadakis E, et al. Risk factors for carbapenem-resistant Klebsiella pneumoniae infection/colonization: a case-case-control study. J Infect Chemother. 2014;20(5):293-297, doi: 10.1016/j.jiac.2013.11.007.
  » https://doi.org/10.1016/j.jiac.2013.11.007
• ²⁸ Maraolo AE, Corcione S, Grossi A, Signori A, Alicino C, Hussein K, et al. The impact of Carbapenem resistance on mortality in patients With Klebsiella pneumoniae bloodstream infection: an individual patient data meta-analysis of 1952 patients. Infect Dis Ther. 2021;10(1):541-558, doi: 10.1007/s40121-021-00408-8.
  » https://doi.org/10.1007/s40121-021-00408-8
• ²⁹ Li Y, Li J, Hu T, Hu J, Song N, Zhang Y, et al. Five-year change of prevalence and risk factors for infection and mortality of carbapenem-resistant Klebsiella pneumoniae bloodstream infection in a tertiary hospital in North China. Antimicrob Resist Infect Control. 2020;9(1):79, doi: 10.1186/s13756-020-00728-3.
  » https://doi.org/10.1186/s13756-020-00728-3
• ³⁰ Fraenkel-Wandel Y, Raveh-Brawer D, Wiener-Well Y, Yinnon AM, Assous MV. Mortality due to blaKPC Klebsiella pneumoniae bacteraemia. J Antimicrob Chemother. 2016;71(4):1083-1087, doi: 10.1093/jac/dkv414.
  » https://doi.org/10.1093/jac/dkv414
• ³¹ Tang H, Zhao Z, Zhang X, Pan L, Wu Q, Wang M, et al. Analysis of pathogens and risk factors of secondary pulmonary infection in patients with COVID-19. Microb Pathog. 2021;156:104903, doi: 10.1016/j.micpath.2021.104903.
  » https://doi.org/10.1016/j.micpath.2021.104903
• ³² Hussein K, Raz-Pasteur A, Finkelstein R, et al. Impact of carbapenem resistance on the outcome of patients' hospital-acquired bacteraemia caused by Klebsiella pneumoniae J Hosp Infect. 2013;83(4):307-313, doi: 10.1016/j.jhin.2012.10.012.
  » https://doi.org/10.1016/j.jhin.2012.10.012
• ³³ Uz Zaman T, Aldrees M, Al Johani SM, Alrodayyan M, Aldughashem FA, Balkhy HH. Multi-drug carbapenem-resistant Klebsiella pneumoniae infection carrying the OXA-48 gene and showing variations in outer membrane protein 36 causing an outbreak in a tertiary care hospital in Riyadh, Saudi Arabia. Int J Infect Dis. 2014;28:186-192, doi: 10.1016/j.ijid.2014.05.021.
  » https://doi.org/10.1016/j.ijid.2014.05.021
• ³⁴ Shibl A, Al-Agamy M, Memish Z, Senok A, Khader SA, Assiri A. The emergence of OXA-48- and NDM-1-positive Klebsiella pneumoniae in Riyadh, Saudi Arabia. Int J Infect Dis. 2013;17(12):e1130-1133, doi: 10.1016/j.ijid.2013.06.016.
  » https://doi.org/10.1016/j.ijid.2013.06.016

Publication Dates

• Publication in this collection
  24 Mar 2025
• Date of issue
  2025

History

• Received
  7 Apr 2024
• Accepted
  8 Feb 2025