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Year : 2022  |  Volume : 9  |  Issue : 4  |  Page : 262-267

Bacteriological Profile and antibiotic susceptibility pattern of tracheal secretions isolates among intensive care unit patients at tertiary care hospital

Department of Microbiology, SVP Hospital, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India

Date of Submission28-Jan-2022
Date of Decision23-Mar-2022
Date of Acceptance14-Apr-2022
Date of Web Publication17-Mar-2023

Correspondence Address:
Atit D Shah
64, Manirathnam Bunglows Part 2, P and T Colony Road, Vasna, Ahmedabad, Gujarat
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/cjhr.cjhr_9_22

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Introduction: Respiratory infections are associated with high morbidity and mortality, especially in critically ill patients. The excessive use of broad-spectrum antibiotics has led to the development of drug resistance, thus resulting in the emergence of pathogens which are difficult to treat. Materials and Methods: A total of 632 tracheal secretions were received in the Bacteriology section of the microbiology department of a tertiary care hospital from November 2019 to February 2020. Tracheal secretions were processed for culture according to standard operating procedures. Identification, phenotype detection, and antibiotic sensitivity testing were performed by automated VITEK-2 Compact system. Results: In total, 632 tracheal secretions were received during the study period, 559 cultures yielded significant pathogens and no organisms were isolated in 73 cultures. Among the Gram-negative organism 540 (97%), Klebsiella pneumoniae (30%) was the most common isolates. Gram-positive organisms 12 (2%) and Candida spp. 7 (1%) were isolated. The most common phenotype detected in Escherichia coli and K. pneumoniae was extended-spectrum beta-lactamase producer. Conclusions: K. pneumoniae was the most common isolate from tracheal secretion among intensive care unit patients. Colistin, followed by tigecycline, was found to be the most susceptible antibiotics. K. pneumoniae was found to be sensitive to tigecycline (69%) with minimum inhibitory concentrations of ≤ 1. 0.6%. K. pneumoniae was colistin resistant.

Keywords: Antimicrobial susceptibility, tracheal secretion, VITEK-2

How to cite this article:
Prajapati BK, Gohel PH, Shah AD, Shah HJ, Kothari KK, Pethani JD. Bacteriological Profile and antibiotic susceptibility pattern of tracheal secretions isolates among intensive care unit patients at tertiary care hospital. CHRISMED J Health Res 2022;9:262-7

How to cite this URL:
Prajapati BK, Gohel PH, Shah AD, Shah HJ, Kothari KK, Pethani JD. Bacteriological Profile and antibiotic susceptibility pattern of tracheal secretions isolates among intensive care unit patients at tertiary care hospital. CHRISMED J Health Res [serial online] 2022 [cited 2023 Mar 31];9:262-7. Available from: https://www.cjhr.org/text.asp?2022/9/4/262/371948

  Introduction Top

Tracheobronchial secretions are produced by mucous glands and goblet cells of the tracheobronchial tree.[1] These secretions are not only involved in the protection of the respiratory system but are also responsible for the exchange of heat and water during breathing.[2]

Respiratory infections are infections of the respiratory tract from the pharynx to the lung parenchyma. The lower respiratory infection occurring in intensive care unit (ICU) patients is associated with high morbidity and mortality.[3] Such patients are commonly maintained using invasive devices which itself tend to be a major reservoir for hospital-acquired infections.[4],[5]

Lower respiratory tract infections (LRTIs) are the most common infectious diseases affecting humans of all age groups. It is responsible for 4.4% of all hospital admissions. It also accounts for 3%–5% of deaths in adults.[6] They are often misdiagnosed, mistreated, and underestimated due to its nonspecific presentation in community or hospital settings. Etiological agents of an LRTI vary according to season and geographic location.[7],[8]

Critically ill patients of ICUs are at greater risk for acquiring hospital-associated infections with multidrug-resistant (MDR) microorganisms. This is because of their prolonged hospital stay, immunocompromised profile, serious illness, use of invasive devices, catheters, and prolonged use of antibiotics.[9] The frequent and unselective usage of broad-spectrum antibiotics without reporting of culture and sensitivity leads to the development of these MDR superbugs and this creates problem for the treatment of ICUs patients.[10],[11]

The longer hospital stay is, for example, head trauma, the more are the chances of a change of bacterial flora causing infection, eventually complicating therapy because of alteration of susceptibility pattern.[12],[13]

Ventilator-associated pneumonia (VAP) is defined as pneumonia that occurs 48–72 h or thereafter following endotracheal intubation, characterized by the presence of a new or progressive infiltrate, signs of systemic infection (fever and altered white blood cell count [WBC]), changes in sputum characteristics, and detection of a causative agent.[14]

VAP is one of the most common and important nosocomial infections, which is acquired by ICU admitted patients, who are intubated for mechanical ventilation. The mechanical ventilation is one of the lifesaving practices for ICU admitted patients, but it has a greater risk of developing respiratory infections. The morbidity of these patients is increased due to the invasion of MDR strains of microorganisms of hospital origin. Among these superbugs, who are associated with pneumonia, are Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella spp., and Acinetobacter spp. Apart from this, ICUs patients developed multibacterial infections during their prolonged stay in hospitals. These changing floras also complicate the therapy by developing MDR and affecting their sensitivities pattern.[15]

Family Enterobacteriaceae comprising Gram-negative (GN) bacteria, their common prevalent bacteria can develop resistance against different beta-lactam agents, which attributes their resistance to broad-spectrum cephalosporin. The antimicrobials of this group were primarily administrated for the treatment of ICUs patients in hospitals previously. Along with them, the bacteria also developed antimicrobial resistance to other groups of antibiotics such as trimethoprim/sulfamethoxazole, fluoroquinolones, and aminoglycosides.[16] Similarly, methicillin-resistant S. aureus (MRSA) strains are also one of the most important microorganisms regarding nosocomial infections in ICUs. MRSA developed due to excessive usage of antibiotics in ICUs settings. About 70% of S. aureus isolated from ICUs are MRSA.[17]

The etiology of these MDR superbugs may vary according to the different ICUs settings along with the patient's illness and their antibacterial treatment. Therefore, it is mandatory to have knowledge about the bacterial pattern of the hospital ICUs settings and their local antimicrobial susceptibility pattern, which provides guidelines to the clinicians for prompt and empirical treatment with appropriate antibiotics.[18]


The objective of this study was to identify the common bacterial pathogens in tracheal secretions and to study the patterns of their sensitivity to various antibiotics.

  Materials and Methods Top

A retrospective study was conducted at tertiary care hospital in Ahmedabad over 4 months, from November 2019 to February 2020. The analysis of the reports was performed at the microbiology department.

Sample collection

The tracheal secretions (bronchoalveolar lavage and endotracheal aspirate) from ICU patients of all the age and sex groups were included in the study.

Patient enrollment: samples from patients admitted in ICU who are on mechanical ventilation for more than 48 h having a clinical history of fever ≥38°C, whose WBCs count ≥11,000/mm3 or ≤4000/mm3, having purulent tracheal secretions and with diffused or patchy infiltration in chest radiograph were included in the study.

Specimen selected in the study

Gram's staining of these samples was done to rule out that whether the bacteria were a colonizer or pathogen using Q-score. It also provided an initial clue about the type of bacteria, whether the material was purulent or not (≥ 25 neutrophils and ≤10 squamous cells per low-power field).

All patients whose quantitative culture had revealed a colony count of <105 colony-forming units (CFU)/ml of tracheal aspirate and who did not show clinical evidence of pneumonia were excluded from the study.

A total of 632 tracheal secretions specimens were enrolled in the study. The received samples of endotracheal secretions were inoculated on blood agar and MacConkey agar and incubated for 24 h in an incubator at 37°C. The cultures were read next day for any positive or negative growth. The culture plates were read semiquantitatively as mild, moderate, or heavy growth. Heavy growth, which corresponds to more than 105 CFU/mL of bacteria, was further studied. The bacteria were preliminarily identified on the basis of their colonial morphology, presence or absence of hemolysis on blood agar, and lactose fermentation on MacConkey agar, whether lactose fermenter or nonfermenter. Then, Gram's staining from the colony was performed to know whether cocci or bacilli are Gram-positive (GP) or GN.

Identification with the VITEK-2 compact system was performed using a GN card and GP card according to the manufacturer's instructions. Antibiotic susceptibility testing with the VITEK-2 compact system was performed using an AST N281 (for Acinetobacter and P. aeruginosa) and N280 (for other GN organisms) susceptibility card for GN organisms and GP628 susceptibility card for GP organisms.[19]

AST card 280 contains antibiotics amikacin, ampicillin, amoxicillin/clavulanic acid, cefepime, cefoperazone/sulbactam, ceftriaxone, cefuroxime, ciprofloxacin, colistin, ertapenem, gentamicin, imipenem, meropenem, nalidixic acid, nitrofurantoin, piperacillin/tazobactam, tigecycline, and trimethoprim/sulfamethoxazole.

AST card 281 contains antibiotics amikacin, cefepime, cefoperazone/sulbactam, ceftazidime, ciprofloxacin, colistin, doripenem, gentamicin, imipenem, meropenem, minocycline, piperacillin/tazobactam, ticarcillin/clavulanic acid, and trimethoprim/sulfamethoxazole.

AST card 628 contains antibiotics ciprofloxacin, clindamycin, daptomycin, erythromycin, gentamicin, levofloxacin, linezolid, nitrofurantoin, oxacillin, rifampicin, teicoplanin, tetracycline, tigecycline, trimethoprim/sulfamethoxazole, and vancomycin.

  Results Top

In total, 632 tracheal secretions were received during the study period, 559 cultures yielded significant pathogens and no organisms were isolated in 73 cultures. Among 559 cultures, 172 samples showed polymicrobial infection.

GN bacteria contributed to the major number of isolates (97%), including K. pneumoniae (30%) being the most common, followed by Acinetobacter baumanni complex (28%), P. aeruginosa. (21%), Escherichia coli (6%) and other GN bacteria include Proteus mirabilis, Providencia rettegeri, Providencia stuartii, Serratia marcescens, Enterobacter cloacae complex, and Stenotrophomonas maltophilia [Chart 1].

GP bacteria (2%) include S. aureus, Staphylococcus hemolyticus, Streptococcus pneumoniae, and Enterococcus faecium. Among Candida spp (1%), Candida tropicalis, Candida famata, Candida albicans and Candida lusitaniae isolated [Chart 1].

In our study, S. aureus is 100% sensitive to vancomycin, linezolid, and tigecycline followed by 85.7% sensitivity to daptomycin [Chart 2].

In our study, Candida spp. showed 100% susceptibility to amphotericin B, caspofungin, flucytosine, fluconazole, micafungin, and voriconazole.

Our results showed that GN bacilli were most susceptible to colistin.

E. coli was sensitive to amikacin (82.3%) with minimum inhibitory concentrations (MIC) ≤ 2, imipenem (67.6%) with MIC ≤ 0.25, meropenem (67.6%) with MIC ≤ 0.25, and tigecycline (94.1%) with MIC ≤ 0.5 [Table 1].
Table 1: Antibiotic sensitivity pattern of Klebsiella spp. and Escherichia coli

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Pseudomonas was sensitive to gentamicin (55.7%) with MIC ≤ 1, cefepime (53.2%) with MIC of 8, amikacin (51.6%) with MIC ≤ 2 [Table 2].
Table 2: Antibiotic sensitivity pattern of Pseudomonas spp. and Acinetobacter spp.

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In our study, phenotypic detection by VITEK-2 AES system; in GP cocci, Staphylococci aureus shows most commonly resistance to penicillin, aminoglycoside, streptogramins, and oxacillin. In GN bacilli, non-lactose fermenter Acinetobacter spp. shows commonly resistance to gentamicin and carbapenems (139) and in Pseudomonas spp. shows common resistance to aminoglycosides and carbapenemase (34) [Table 3].
Table 3: Relevant phenotype study by VITEK-2 advanced expert system

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In lactose fermenter organisms E. coli and K. pneumoniae, the most common phenotype is extended-spectrum beta-lactamase (ESBL) producing [Table 3].

  Discussion Top

The resistance to conventional antibiotics is severely increasing in bacteria in clinical and nonclinical settings.[20] The rate of nosocomial infection is also increasing in the patients admitted to the ICU due to excessive invasive procedures performed, including artificial ventilator support.[21] This constantly emerging resistance is a serious situation implying the need for new regulations for the cautious use of antibiotics and refining the conditions of hospitals to prevent further exacerbation of resistance shown by the bacteria.

The percentage of samples showing positive growth in our study was 88.4%. In a study by Chandra et al., the positive samples were 72.3%.[18] In a study conducted by Malik et al., the positive cultures came out to be 83%.[22] Organisms not isolated in samples may be due to the inability to culture fastidious organisms or anaerobic organisms.

In our study, GN bacilli were more common causative agents (97%) as compared to GP cocci, which were (2%) of the total positive cultures. Similar findings are observed in a study by Chandra et al., in which the GN bacilli were 85% and in a study by Gupta et al., in which 86% of the samples were GN bacilli.[18],[23] A study by Chandra et al. showed that more of the isolates from the patients were GN enteric aerobic bacteria, with Klebsiella being the most common species, followed by Acinetobacter and Pseudomonas.[18] The GN predominance might partly be due to the unequal distribution of patients with community-acquired and hospital-acquired infections and also due to the spread of antibiotics resistance in hospital settings. This can be attributed to the fact that the majority of nosocomial infections are caused by GN bacteria, which are difficult to treat. This calls for strict measures against the spread of GN bacilli, especially in the ICU setting.

In our study, K. pneumoniae (30.2%) was the most common isolate, followed by Acinetobacter spp.(28%). In a study by Malik et al., the most common bacterium isolated from tracheal secretions was K. pneumoniae (35.4%).[22] Furthermore, in a study by Chandra et al., Klebsiella (32.35%) was the most common isolate.[18] Because of their ability to spread rapidly in the hospital environment, K. pneumonia tends to cause nosocomial outbreaks.

In our study, among GN bacteria, Klebsiella isolates and Acinetobacter spp. were resistant to group of antibiotics, namely cephalosporins and aminoglycosides. The most common phenotype in Klebsiella was resistant to aminoglycosides, carbapenemase producing, and impermeability carbapenem, while in Acinetobacter spp. phenotype was resistant to aminoglycosides and carbapenemase producing. This might be due to continuous exposure of these bacteria to a variety of beta-lactams that leads to the production of beta-lactamases. Moreover, plasmid- and chromosomal gene-mediated beta-lactamase enzymes are major reasons for antibiotic resistance.

Klebsiella was most sensitive to colistin, followed by tigecycline with the most common MIC of 1, and then amikacin with MIC of ≤2. Acinetobacter spp. was most sensitive to colistin, followed by tigecycline with the most common MIC of 1, followed by minocycline with an MIC of ≤1.

On the other hand, E. coli was the least resistant organism being sensitive to colistin, imipenem, meropenem, and tigecycline. The most common phenotype most was ESBL.

In Pseudomonas spp., the most common pattern is resistance to aminoglycosides and carbapenemase. Among these, colistin is the most sensitive drug for Pseudomonas, followed by gentamicin with MIC of < = 1.

Among GP bacteria, S. aureus was shown to 100% susceptibility to higher antibiotics, namely teicoplanin, linezolid, vancomycin, and tigecycline. While resistance was observed toward co-trimoxazole, oxacillin, benzylpenicillin, and fluoroquinolones.

It is necessary to have policies regarding the restrictive use of antibiotics such as aminoglycosides and carbapenems. Regular monitoring of such resistant isolates would be important for infection control in critical units.

  Conclusions Top

In our study, GN bacilli were more common causative agents (97%) as compared to GP cocci, which were (2%) of the total positive cultures. Among GN bacteria, K. pneumoniae (30.2%) was the most common isolate, followed by Acinetobacter spp. (28%). Klebsiella isolates and Acinetobacter spp. were resistant to antibiotics, namely cephalosporins and aminoglycosides. The most common phenotype in Klebsiella was resistant to aminoglycosides, carbapenemase producing, and impermeability carbapenem, while in Acinetobacter spp., phenotype was resistant to aminoglycosides and carbapenemase producing. Proper identification of the pathogens and their antibiotic susceptibility pattern with MIC can help our health professionals to choose the right antibiotic therapy and improve the outcome.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

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  [Table 1], [Table 2], [Table 3]


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