The clinical impact of bacterial co-infection among moderate, severe and critically ill COVID-19 patients in the second referral hospital in Surabaya

Introduction

Coronavirus disease (COVID)-19 has experienced an increase in 2,995,758 positive cases and 204,987 deaths in distribution areas of more than 213 countries¹. In Indonesia, until November 2020, there were 522,581 confirmed cases of COVID-19 with 68,604 active cases, 437,456 recovered cases, and 16,521 (3%) deaths. According to national data, among the total number of cases, East Java is the second-highest prevalence of 60,190 (11.6%). As of November 26, 2020, the cumulative data on confirmed COVID-19 patients in Surabaya were 16,763 with 1204 (7.03%) deaths¹.

Data regarding secondary respiratory infection in COVID-19 patients are still limited even though cases distribution is still worldwide. Several reports suggest that secondary infection will impact the patient’s survival and increase intensive care unit (ICU) treatment². COVID-19 pneumonia itself is also related to increasing ICU care, secondary infection rate, and higher invasive treatment³. Co-infection of SARS-CoV-2 and other microorganisms such as viruses, bacteria, and fungi is an essential factor in COVID-19 treatment since this condition may raise the difficulty in diagnosis, treatment, and the prognosis, also increasing the mortality^4,5. Upper respiratory tract infection, a typical manifestation of COVID-19, is challenging to differentiate from other causes of pneumonia.

There are various types of co-infection in COVID-19; such as: 1) secondary SARS-CoV-2 following bacterial infection or colonization; 2) mixed infection between viral and bacterial pneumonia infection; 3) secondary bacterial superinfection following SARS-CoV-2 infection. The mechanisms underlying those types of infection are very dependent on the onset and involving complex interactions between three different agents (virus, host, and bacteria). Immune response towards SARS-CoV-2 infection only differs with mixed infection to bacteria or viral pneumonia. Therefore, it could be hypothesized that any co-infection will worsen the outcome and severity of COVID-19⁶.

Although several studies have investigated the epidemiological and clinical characteristic of COVID-19, information regarding SARS-CoV-2 infection with secondary infection are limited⁷. This study aims to describe bacterial co-infection and antibiotic use among patients who confirmed SARS-CoV-2 infection from moderate to critically ill manifestation in Universitas Airlangga hospital Surabaya.

Methods

Results

Bacterial infections

Bacterial infection was confirmed in 43 patients (19.7%) (see Table 2). There were no sex differences between bacterial infection and no bacterial infection patients. Patients with a bacterial infection have an older mean age than no bacterial infection, although, among elderly patients, there were no differences in bacterial infection rate. We documented one patient with chronic obstructive pulmonary disease (COPD) and one with liver disease as a comorbidity, and both of them suffered from bacterial infection. Other comorbidities such as diabetes, hypertension, heart disease, stroke, chronic kidney disease did not differ between the two categories. COVID-19 patients with bacterial infections had a longer hospital length of stay, a higher proportion of respiratory failure, ICU treatment, ventilator use.

Table 2. Comparison of COVID-19 patients who had bacterial infections and without bacterial infections.

	Bacterial Infection		No Bacterial Infection		Total (n.%)		p value
	43		175		218	100
Sex
Male (n=35)	20	29.85	100	45.90	120.00	75.75	0.21
Female (n=32)	23	34.33	75	34.40	98.00	68.73
Age(Mean/SD)	55.28	12.98	51.76	14.72	52.45	14.44	0.153
Comorbidities
HT (n.%)	18	8.30	47	21.60	65.00	29.90	0.054
DM (n.%)	15	6.90	60	27.50	75.00	34.40	0.94
Geriatric (> 60 years) (n.%)	12	5.50	47	21.60	59.00	27.10	0.89
Heart disease (n.%)	4	1.80	10	4.60	14.00	6.40	0.39
CKD (n.%)	2	0.90	7	3.20	9.00	4.10	0.85
Stroke (n.%)	1	0.50	10	4.60	11.00	5.10	0.36
COPD (%)	1	0.50	0	0.00	1.00	0.50	0.043
Liver disease (n.%)	1	0.50	0	0.00	1.00	0.50	0.043
Smoker (n.%)	1	0.50	6	2.80	7.00	3.30	0.42
ICU room (n.%)	22	10.1	14	6.4	36.00	16.50	<0.05
Respiratory Failure (n.%)	14	6.4	29	13.3	43.00	19.70	0.018
Ventilator (n.%)	9	4.1	14	6.4	23.00	10.50	0.013
Sepsis (n.%)	7	3.2	10	4.6	17.00	7.80	0.021
Antibiotic use	36	16.5	128	58.7	164.00	75.20
Length of stay (mean/SD)	17.6	6.62	13.31	7.12			<0.05
Outcome (between group)
Discharge (n.%)	35	81.40	148	84.57	183.00	165.97	0.04
Death (n.%)	7	16.28	14	8	21.00	24.28

Mortality occurs in 16.28% of COVID-19 patients with bacterial infections, higher than those without bacterial infection (8%). Overall, COVID-19 patients with bacterial infection had a worse prognosis than those without bacterial infection (p<0.04).

The empirical antibiotic was given to 75.2% of the patients. Antibiotics used in these patients were quinolones (60.1%), cephalosporins (28.44%), carbapenem (23.85%), and aminoglycosides (4.59%). Quinolone used in these patients was mostly levofloxacin (79.39%), and the others were moxifloxacin (20.61%). The carbapenem used in this study was meropenem. Cephalosporins used were ceftriaxone, ceftazidime, cefotaxime, cefoperazone-sulbactam, and cefuroxime (see Figure 1).

Figure 1. The empirical antibiotic use in study population.

Pathogens associated with a bacterial infection

We collected 110 culture samples from suspected bacterial infection patients, consisting of 44 blood samples, nine urine samples, and 57 sputum samples. Among them, bacteria were detected in nine blood cultures, four urine cultures, and 47 sputum cultures. Sputum samples were collected, some from spontaneous sputum (n=47) and the others from endotracheal tube aspirate (n=10). Gram-negative bacteria dominate the culture result (70.37%). Bacteria found in the blood were extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae (2), Pseudomonas fluorescens (1), Pseudomonas putida (1), Staphylococcus epidermidis (2), Staphylococcus haemolyticus (1), Staphylococcus hominis (2). Bacteria found in urine were ESBL-producing Escherichia coli (2), Enterococcus faecalis (1), and Pseudomonas putida (1). There were 47 isolates found in sputum cultures, in which six of them were fungi (Candida spp). The most frequent bacteria found was Acinetobacter baumannii (9), followed by Klebsiella pneumoniae (5), Pseudomonas aeruginosa (4), Escherichia Coli (2), Enterobacter cloacae complex (3), and Staphylococcus haemolyticus (3) (see Table 3 and Figure 2).

Table 3. Result of microbiological culture.

Culture	Number
Sputum	57
Acinetobacter baumannii	9
Candida spp.	6
Klebsiella pneumoniae	5
Pseudomonas aeruginosa	4
Enterobacter cloacae complex	3
Staphylococcus haemolyticus	3
Streptococcus mitis / Streptococcus oralis*	3
Escherichia coli	2
Escherichia coli (ESBL)	1
Others	11
No growth	10
Blood	44
Klebsiella pneumoniae (ESBL+)	2
Staphylococcus epidermidis*	2
Staphylococcus hominis*	2
Pseudomonas flurescens	1
Pseudomonas putida	1
Staphylococcus haemolyticus	1
No growth	35
Urine	9
Escherichia coli (ESBL)	2
Enterococcus faecalis	1
Pseudomonas putida	1
No growth	5

Note : *, considered as normal flora bacteria.

Figure 2. Distribution of Gram-positive and Gram-negative bacteria.

Discussion

Our study focuses on bacterial infection results in COVID-19 patients and evaluates their clinical and microbiological features. Clinical characteristics of the study group were described according to disease severity. According to disease severity, the number of patients with moderate, severe, and critically ill manifestations were 126 (57.8%), 40 (18.3%), and 52 (23.9%), respectively. The average age was 52.45 (±14.44) years, and 55.05% of patients were male. Other studies regarding the characteristic of hospitalized COVID-19 patients showed various results. Zhou et al. reported that the median age of the 191 patients was 56.0 years (18–87 years), and most patients were male¹¹. Lv et al. reported 354 hospitalized patients, 175 (49.44%) were male, and the median age was 62 years (23–90 years)¹². A study conducted in Saudi Arabia reported among the 99 hospitalized patients, the median age was 44 years (range 19–87), and the majority were men (66%)¹³. We found that diabetes and hypertension were the most common comorbidity, similar to these other studies^11–14.

In this study, inflammation signs such as leukocyte count, neutrophil count, procalcitonin in the critically ill group were higher than the others. Lymphopenia in COVID-19 patients occurs through various mechanisms such as direct virus invasion lymphocytes, lymphatic organ destruction, altered inflammatory cytokines production leading to lymphocyte apoptosis, and inhibiting lymphocytes function by metabolic molecules produced by metabolic disorders, such as hyperlactic academia¹⁵. Neutrophil and lymphocyte ratio (NLR) has been proposed as a prognostic marker of severity in various chronic inflammatory diseases, including cardiovascular diseases and oncological processes¹⁶.

Our result showed a significant increase of procalcitonin level and a higher proportion of bacterial infection in severe and critically ill COVID-19 patients. This finding is consistent with the study result from Wang et al. in elderly COVID-19 patients. They also concluded that bacterial infection was also considered as a predictor of mortality in these patients¹⁷. Increased procalcitonin level in COVID-19 patients may be associated with the release of some cytokines, especially IL-6. It is established that procalcitonin is a better marker to predict severity, prognosis, or the sepsis course and is also helpful to guide antibiotic usage. Increased procalcitonin in critically ill patients with COVID-19 can represent a bacterial co-infection, and blood cultures for bacteria detection are needed to a prompt response¹⁸.

In this study, we found that bacterial infection was confirmed in 43 patients (19,7%). The bacterial infection that was detected at patient admission (bacterial co-infection) was 23%, while bacterial infection that occurs late during hospital stay (secondary infection) was 77%. The prevalence of bacterial co-infections in patients admitted to the ICU for acute respiratory failure related to COVID-19 pneumonia is poorly studied^19,20. In Fu et al. study, 13.9% (5 of 36) of the patients in the ICU were diagnosed with COVID-19 and secondary bacterial infection. In another report that was published from a UK secondary care setting, 27 among 836 patients (3.2%) had early confirmed bacterial isolates identified (0–5 days post-admission), rising to 51 cases (6.1%) during the admission. In a study conducted in Shiraz, Iran, in 2009, Hassanzadeh et al. suggested that ICU-acquired infections were documented in 51.7% of ICU patients, with a mortality rate of 10.9% (5 patients)^21,22. Our finding was relatively higher among other studies. The possible explanation is that most of the patients had been treated in hospital for more than two weeks (average 12–17 days). Secondary infections usually correspond with nosocomial or healthcare-associated infections. Nosocomial infections are most commonly correlated with invasive medical devices or surgical procedures. Lower respiratory tract and bloodstream infections have the highest mortality, while urinary tract infections are the most common²³.

The median length of stay among patients in our study was higher in the bacterial co-infection group rather than non co-infection, with an average of 17.6 and 13.31 days, respectively. This finding is consistent with the result of several studies^21,24. Sharifpour et al. reported that the median length of stay is around 15 days (interquartile range, 2 to 39). A study on respiratory co-infection in patients with pandemic 2009 influenza A (H1N1) virus infection showed that ICU length of stay was three days longer among patients with co-infection. Another study by Zhou et al. reported a longer length of stay of 8.0 days (4.0–12.0) of all patients with COVID-19 admitted to their ICU¹¹. These findings suggest that the length of ICU stay can be prolonged if patients become co-infected.

The most common bacterial infection in this study was from respiratory tract infection, followed by bloodstream infection and urinary tract infection. The culture result was dominated by gram-negative bacteria (75.68%). This finding is similar to the result from Zhang et al. (50%), although they also included virus and fungal cultures³. Gram-negative bacteria were reported responsible for more than 30% of healthcare-associated infections, and these bacteria predominate in cases of ventilator-associated pneumonia (47%) and urinary tract infections (45%)²³. In intensive care units (ICUs), gram-negative bacteria account for about 70% of these types of infections²⁵. Gram-negative bacteria are highly efficient at up-regulating or acquiring genes that code for antimicrobial resistance mechanisms, especially in the presence of antibiotic selection pressure. Among gram-negative bacteria, the Enterobacteriaceae family being the most commonly found and multidrug-resistant organisms, including Pseudomonas aeruginosa, Acinetobacter baumannii, and extended-spectrum β- lactamase (ESBL)–producing or carbapenemase-producing Enterobacteriaceae, are increasingly being reported worldwide²³. The identification of bacterial infection with gram-negative organisms is more reflected as a complication of ICU care and is not suggested as a specific predilection for co-infections in COVID-19²².

Acinetobacter baumannii is the most common bacteria found in this study. Several reports regarding bacterial infection in COVID-19 also found a similar result^3,7,9,18,23. Acinetobacter baumannii is the common cause of respiratory tract infection, especially in ICU settings where patients often received mechanical ventilation. Environmental contamination also plays a role in this phenomenon. Our ICUs for COVID-19 patients were set as a large ward consist of 16 beds. Although we already managed the distance between beds for more than 1.5 meters, the inter-patient transmission is hard to avoid. It is crucial to maintain hand hygiene compliance of the staff, strict cleanliness, and disinfection of the hospital environment in the hospital, especially in high-care or ICU setting.

Antibiotic is often given to COVID-19 patients for various reasons. The clinical manifestation on presentation was sometimes challenging to distinguish with bacterial infection². Secondary infection and nosocomial infection are also other considerations in the use of antibiotics. In this study, 75.3% of patients included were given antibiotics. A meta-analysis conducted about bacterial co-infection and secondary infection in COVID-19 patients reported that the majority of patients with COVID-19 received antibiotics (71.9%, 95%CI 56.1 to 87.7%)²⁶. Another meta-analysis reported that >90% of COVID-19 patients were given an empirical antibiotic, while the bacterial infection was detected only in 7% of hospitalized patients and 14% of ICU patients²⁷. Quinolones (levofloxacin and moxifloxacin) were frequently prescribed, followed by cephalosporins and carbapenems. Indonesian national guidelines for COVID-19 treatment recommend using antibiotics in severe and critically ill patients, especially if there was suspicion of bacterial infection. The empirical antibiotic choice was intravenous azithromycin or levofloxacin¹⁰. In our hospital, levofloxacin is more feasible than azithromycin, so clinicians prefer to prescribe this drug. In our hospital, antibiotic use usually was decided based on clinical signs and laboratory parameters (leukocytosis, increased CRP, or procalcitonin). Culture examinations were not routinely performed, preferably in ICU/high-care settings and in patients showing bacterial infection.

The widespread use of antibiotics in this pandemic era raises concern about antimicrobial resistance^4,6. Although bacterial infection in COVID-19 patients has already been reported in various results, evidence supports the restrictive use of antibiotics. Clinical guidelines and standard testing to diagnose bacterial infection in COVID-19 are not clearly available. The microbiological examination is an important strategy to confirm bacterial infection and decide the antibiotic choice⁴. Sputum, blood culture samples, and also pneumococcal urinary antigen testing should also be performed. Antibiotics should be stopped in patients who represent cultures, and urinary antigen tests show no signs of bacterial pathogens after 48 hours²⁸.

There are some limitations to our study. First, we only included COVID-19 patients in high-care and intensive care units. In low-care settings, bacterial infection cannot be confirmed due to limited data. Second, we only reported bacterial infection from microbiology results. Virus culture or gene sequencing to detect pathogens is not available in our hospital. Bacterial culture was not performed in all COVID-19 patients, so in a condition where the sign of infection is absent such as in elderly or in immunocompromised patients, the bacterial infection might be underdiagnosed.

Conclusions

Bacterial infection was detected in 19.7% of COVID-19 patients admitted in high-care and intensive care units, predominantly secondary infections. COVID-19 patients who suffered from bacterial infection have a longer length of stay and have higher mortality. The pathogen commonly found in this study was Acinetobacter baumannii that yielded from sputum. Increased antibiotic use and multi-drug resistant organism is an emerging problem in this pandemic situation. Infection control practice need to strictly conducted to reduced secondary or healthcare-associated infection

Data availability