Prevalence of Antimicrobial Resistant Pathogens in Severe Sepsis and Septic Shock Patients

Babu, Menon, and Uma: Prevalence of Antimicrobial Resistant Pathogens in Severe Sepsis and Septic Shock Patients

Authors

INTRODUCTION

The emergence of antimicrobial resistance is increasing at an alarming rate worldwide1 and is becoming a serious threat to public health.2-3 India can face dire consequences since it is the world’s largest consumer of antibiotics.4 Antibiotic overuse, inappropriate prescribing, extensive uses in poultry, poor infection control, have all contributed to the above phenomenon.2,5 The emergence of multidrug resistance (MDR) especially in gram negative microbes like Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii has left clinicians with fewer treatment options, contributed to more healthcare resources and worst clinical outcomes.2,6-7 Sepsis, resulting due to impairment of host defences to infection,8-9 requires prompt implementation of antibiotic therapy to reduce morbidity and mortality.10 Epidemiological studies have reported an increase in the incidence of severe sepsis and septic shock11-12 with even gram positive and fungal organisms being the causative agents.13 Thus, it is essential to have knowledge about the local epidemiological pattern among the severe sepsis and septic shock patients since the organisms causing sepsis may not only vary based on regions but also change over time. Our study aims to assess the microbiological and susceptibility patterns of isolates obtained from severe sepsis and septic shock patients.

MATERIALS AND METHODS

This was a prospective, observational study conducted at our hospital from April 2015-16. Adut patients with a diagnosis of severe sepsis/septic shock were included in the study cohort, and only the first episode of severe sepsis or septic shock was counted. This study was approved by the institutional review board of the hospital (Thesis review committee/Pharma/2015/20). Being an observational study without any direct patient contact, the need for informed consent was waived. We used a case report form to collect data. In regard to microbiology results, cultures without any significant growth after the standard incubation period allotted for a particular specimen or cultures growing contaminants were classified as negative culture. A total of 293 isolates were recovered from the 250 enrolled patients. The clinical specimens included blood, urine, skin/soft tissue, and respiratory specimens. The isolates were identified by Vitek 2 Compact system (Biomerieux, France). All laboratory methods followed standard protocols. The susceptibility testing was done by both Kirby Bauer’s disc diffusion and broth dilution methods as per Clinical and Laboratory Standards Institute (CLSI) guidelines.

RESULTS

Patient demographics and specimen types

In the present study, clinical specimens of 250 adult patients [203 severe sepsis and 47 septic shock] from our tertiary care hospital were evaluated. The patient age distribution was as follows: 18 to 40 years, 10.6% (31/293); 41 to 60 years, 40.6% (119/293); 61 to 80 years, 41.3% (121/293); >80 years, 7.5% (22/293). Out of 293 isolates, 204 were from males. One hundred and seventy eight (147 severe sepsis and 31 septic shock) patients had a positive culture. Majority of the patients [44.8% (112/250)] suffered from monomicrobial infection, while 66 patients (26.4%) suffered from polymicrobial infections. One hundred and thirty one patients had a single site infection while 47 patients had multiple site infections. Overall, 293 isolates were obtained (240 isolates from severe sepsis patients and 53 isolates from septic shock patients). With regard to specimen source, 38.6% (113/293) of the organisms were obtained from urine specimens, 27% (79/293) from blood, 16.4% (48/293) from skin/soft tissue specimens, and 15% (44/293) from respiratory specimens. The remaining organisms were obtained from ascitic/peritoneal fluid, synovial fluid and bone.

Most common microorganisms isolated

In the present study, gram negative organisms were predominant (177/293, 60.4%) followed by gram positive (68/293, 23.2%) and fungi (48/293, 16.4%). Overall, the most common isolates were Escherichia coli (20.8%), Klebsiella pneumoniae (18.8%), Pseudomonas aeruginosa (7.8%), Candida albicans (6.1%) and Candida non-albicans (5.8%). The most common isolates among severe sepsis patients were Escherichia coli (52/240, 21.7%), Klebsiella pneumoniae (44/240, 18.3%), Pseudomonas aeruginosa (21/240, 8.8%), Candida albicans (15/240, 6.3%), Candida non-albicans (14/240, 5.8%). The most common isolates among septic shock patients were Klebsiella pneumoniae (11/53, 20.8%), Escherichia coli (9/53, 17%), Candida albicans (3/53, 5.7%), Candida non-albicans (3/53, 5.7%) and Candida tropicalis (3/53, 5.7%). The distribution of prevalent microbial species were found to be similar between patients with severe sepsis and septic shock.

Most common microorganisms isolated from specimen site

Overall, 113 isolates were obtained from urine specimens (91 isolates from severe sepsis patients and 22 isolates from septic shock patients). Among urinary tract specimens, Escherichia coli (20.4%), Klebsiella pneumoniae (18.6%) and Candida non-albicans (13.3%) were the predominant organisms. In patients with severe sepsis, Klebsiella pneumoniae (19/91, 20.9%) was the main isolate from urine specimen followed by Escherichia coli (18/91, 19.8%) and Candida non-albicans (12/91, 13.2%). The main isolates from the urine specimen of septic shock patients were Escherichia coli (5/22, 22.7%), Candida albicans (3/22, 13.6%) and Candida non-albicans (3/22, 13.6%).

Within the blood specimens, 79 isolates were obtained (65 isolates from severe sepsis patients and 14 isolates from septic shock patients). The predominant isolates were Escherichia coli (30.4%), Klebsiella pneumoniae (20.3%) and Staphylococcus aureus (8.9%). In patients with severe sepsis, the main isolate from blood specimen was Escherichia coli (21/65, 32.3%) followed by Klebsiella pneumoniae (11/65, 16.9%). The main isolates from the blood specimen of septic shock patients were Klebsiella pneumoniae (5/14, 35.7%) and Escherichia coli (3/14, 21.4%).

With regard to skin/soft tissue specimens, 48 isolates were obtained (40 isolates from severe sepsis patients and 8 isolates from septic shock patients). Escherichia coli (16.7%), Klebsiella pneumoniae (10.4%) and Pseudomonas aeruginosa (8.3%) were the most commonly isolated organisms. In patients with severe sepsis, Escherichia coli (8/40, 20%) and Pseudomonas aeruginosa (4/40, 10%) were the common isolates whilst in septic shock patients, the predominant isolate was Klebsiella pneumoniae (2/8, 25%).

A total of 44 isolates were obtained from respiratory specimens (39 isolates from severe sepsis patients and five isolates from septic shock patients). In patients with severe sepsis, Klebsiella pneumoniae (10/39, 25.6%), Candida albicans (9/39, 23.1%) and Pseudomonas aeruginosa (9/39, 23.1%) were the most common organisms isolated. The organisms isolated from the respiratory specimen of septic shock patients were alpha haemolytic streptococci, Candida tropicalis, Candida glabrata, Chromobacterium violaceum and Acinetobacter baumannii (1/5, 20% each).

Antimicrobial susceptibility

Antimicrobial resistance rates for the most common gram negative organisms are listed in Table 1. Escherichia coli showed high resistance against amoxicillin-clavulanate, ampicillin-sulbactam, ceftriaxone and ciprofloxacin. However, it showed good susceptibility to amikacin, meropenam and piperacillin-tazobactam. More than 60% of the isolated Klebsiella pneumoniae strains were resistant to most of the antibiotics tested. Pseudomonas aeruginosa showed high resistance to ciprofloxacin (47.8%) and gentamicin (47.8%). Acinetobacter baumannii showed ≥75% resistance to amikacin, ampicillin-sulbactam, ciprofloxacin, cotrimoxazole, gentamicin, meropenam and piperacillin-tazobactam.

Table 1

Resistance rates for the top five gram negative organisms.

OrganismAMIAMOX-CLAVAMP-SULBCEFTRCIPROCOLICOTRIGENTMERPIPTTIG
Escherichia coli3/59
(5.1)
50/58
(86.2)
43/57
(75.4)
44/60
(73.3)
41/57
(71.9)
-26/60
(43.3)
24/58
(41.4)
1/15
(6.7)
5/43
(11.6)
-
Klebsiella pneumoniae28/51
(54.9)
40/52
(76.9)
34/54
(63)
34/54
(63)
33/51
(64.7)
1/30
(3.3)
33/54
(61.1)
33/53
(62.3)
21/34
(61.8)
28/36
(77.8)
6/11
(54.5)
Pseudomonas aeruginosa9/22
(40.9)
---11/23
(47.8)
1/9
(11.1)
-11/23
(47.8)
5/13
(38.5)
3/15
(20)
-
Acinetobacter baumannii6/8
(75)
-6/8
(75)
-7/8
(87.5)
-6/8
(75)
6/7
(85.7)
6/7
(85.7)
7/8
(87.5)
1/4
(25)
Proteus mirabilis--1/1
(100)
1/1
(100)
-------

AMI = amikacin, AMOX-CLAV = amoxicillin-clavulanate, AMP-SULB = ampicillin-sulbactam, CEFTR = ceftriaxone, CIPRO = ciprofloxacin, COLI = colistin, COTRI = cotrimoxazole, GENT = gentamicin, MER = meropenam, PIPT = piperacillin-tazobactam, TIG = tigecycline.

Resistance rates for the most common gram positive organisms are listed in Table 2. Staphylococcus aureus showed high resistance to penicillin G (83.3%) and ciprofloxacin (100%). Enterococcus faecium showed 100% resistance to ampicillin, amoxicillin, erythromycin, ciprofloxacin, ofloxacin and penicillin G.

Table 2

Resistance rates for the top five gram positive organisms.

OrganismAMP/
AMOX
CIPROCLINDCLOX/
OXA
COTRIERYNITROOFLOPEN GTET
Staphylococcus aureus-1/1
(100)
2/6
(33.3)
5/12
(41.7)
4/12
(33.3)
1/2 (50)--10/12
(83.3)
-
Enterococcus species7/9
(77.8)
3/3
(100)
---3/3
(100)
6/8
(75)
4/4
(100)
6/8
(75)
1/7
(14.3)
Enterococcus faecalis2/9
(22.2)
2/2
(100)
1/1
(100)
--3/4
(75)
1/5
(20)
3/4
(75)
2/10
(20)
-
Enterococcus faecium7/7
(100)
2/2
(100)
---1/1
(100)
3/5
(60)
2/2
(100)
7/7
(100)
2/3
(66.7)
Streptococcus species-----2/5
(40)
-1/6
(16.7)
1/5
(20)
-

AMP/AMOX = ampicillin/amoxicillin, CIPRO = ciprofloxacin, CLIND = clindamycin, CLOX/OXA = cloxacillin/oxacillin, COTRI = cotrimoxazole, ERY = erythromycin, NITRO = nitrofurantoin, OFLO = ofloxacin, PEN G = penicillin G, TET = tetracycline.

Multi drug resistance (MDR)

Overall, 47 patients (41 severe sepsis and 6 septic shock) suffered from MDR infection. Out of the Klebsiella pneumoniae isolates tested, 56.4% (31/55) showed MDR. The MDR phenotype occurred in 24.6% (15/61) of Escherichia coli and 30.4% (7/23) of Pseudomonas aeruginosa. Acinetobacter baumannii showed high rates of MDR (87.5%). In the present study, 79 patients (39 severe sepsis and 40 septic shock) expired. Of these 79 expired patients; 20 patients had negative culture, 29 patients had monomicrobial infection and 30 patients had polymicrobial infection. Of the 47 patients with MDR infection, 18 patients (12 severe sepsis and 6 septic shock) expired. Among the fungal isolates, no resistance was observed. Among the Staphylococcus aureus isolates, 38.5% (5/13) showed methicillin resistance.

DISCUSSION

During the period of 2015-16, the clinical samples of 250 severe sepsis and septic shock patients was analyzed for the presence of microorganisms. Traditionally, respiratory infections were considered to be the main cause of severe sepsis and septic shock.12,14 However, in the present study, urinary tract was the major infectious site. Ours being a tertiary care hospital, majority of our patients were referred cases and had Foley’s catheter on admission in our hospital. This could be one of the reason for the high proportion of urinary isolates observed in our study.

Previously, sepsis was considered to be related with gram negative bacteria only. However, some epidemiological studies have shown that even gram positive organisms and fungi could be common causes of sepsis.13 In patients with severe sepsis and septic shock, prompt treatment of infection is the cornerstone of therapy and predictive of survival.10 To select the right antimicrobial for the offending pathogen, knowledge of the causative organisms and their local antimicrobial susceptibility patterns is pivotal. In the present study, the vast majority of isolates were Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. High rates of MDR among the gram negative isolates were observed in the present study, which represents an increasing threat to patients. High resistance was seen among the Escherichia coli species against amoxicillin-clavulanate, ampicillin-sulbactam, ceftriaxone and ciprofloxacin. Escherichia coli is posing a threat as these resistant strains have the ability to transfer resistant determinants not only to their own strains but also to other bacteria present in the gastrointestinal tract. In our hospital setting, Klebsiella pneumoniae and Acinetobacter baumannii showed high rates of resistance to majority of the agents. Thus, the treatment options for MDR Klebsiella pneumoniae appears to be limited to combination therapy with some aminoglycosides, tigecycline and to older antimicrobial agents like colistin. Acinetobacter baumannii too appeared to have a high capacity to acquire antibiotic resistance. This may be because it has different mechanisms of resistance such as antimicrobial inactivating enzymes (eg., beta-lactamases), reduced access to bacterial targets (eg., altered porin channels), efflux pumps, aminoglycoside modifying enzymes etc.15 Piperacillin-tazobactam and meropenem showed effectiveness against Pseudomonas aeruginosa.

CONCLUSION

Our results highlight the high prevalence of gram negative organisms among severe sepsis and septic shock patients in south India. Strict implementation of sepsis guidelines, right antibiotic selection and dosage will help in preventing the development of resistance.

ACKNOWLEDGEMENT

This study was supported by a grant from the Kerala State Council for Science, Technology and Environment.

CONFLICT OF INTEREST

The authors declare that they have no competing interests.

ABBREVIATIONS

CLSI

Clinical and Laboratory Standards Institute

MDR

Multidrug resistance.

SUMMARY

A high prevalence of gram negative organisms were seen, with Escherichia coli being the most common isolate. A high rate of multidrug resistance was observed especially in Acinetobacter baumannii and Klebsiella pneumoniae.

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