Original Article

Isolation of obligate anaerobes from clinical samples received for routine bacterial culture and sensitivity: a cross sectional study


Background and Objectives: Obligate anaerobic bacteria are known to cause various infections in human beings. We aimed to determine the prevalence and spectrum of obligate anaerobes encountered in pus aspirate, sterile fluids and tissue samples received for routine bacterial culture and sensitivity.
Materials and Methods: A total of 160 samples including tissue, sterile body fluids and pus aspirate were collected , analysed for prevalence and spectrum of obligate anaerobes. Identification of obligate and facultative anaerobes was done by automated MALDI-TOF and Vitek 2 method.
Results: Among 160 samples, 75 samples (46.8%) yielded obligate anaerobes out of which 41 samples (26%) yielded obligate anaerobes along with facultative anaerobes which was significant (p value=0.031) and 34 samples (21%) yielded only obligate anaerobes. 90 obligate anaerobes were isolated from 75 samples among which only 34 (37.7%) samples yielded only obligate anaerobes and 56 (62.2%) yielded both obligate and facultative anaerobes. Gram stain with polymicrobial appearance (p value 0.02) was found to be significantly associated with growth of obligate anaerobes. Clinical conditions where obligate anaerobes were commonly associated were appendicular abscess, empyema, fournier’s gangrene, diabetic foot, ludwigs angina and deep abscess. Out of 75 positive samples 30 (40%) patients had predisposing conditions like diabetes mellitus, hypertension etc. Total of 90 obligate anaerobes and 49 facultative anaerobes were isolated. The common obligate anaerobes were Bacteroides fragilis 18 (20%), Prevotella spp. 20 (22.2%), and Clostridium spp. 8 (8.88%). Facultative anaerobes like Escherichia coli 25 (34.7%), Klebsiella species 15 (20.8%), Enterococcus faecalis 19 (26.3%) were isolated. Antibiotic sensitivity was performed for facultative anaerobes by Kirby bauer disc diffusion method. Out of 15 Escherichia coli isolates resistance was commonly seen for ampicillin 13 (86.6%), cephalosporins 11 (73.3%), ciprofloxacin 10 (66.6%) and Piperacillin tazobactum 8 (53.3%). In Klebsiella species resistance were commonly seen to Ampicillin 6 (100%), cephalosporins 2 (33.3%) and ciprofloxacin 2 (33.3%).
Conclusion: There was significant isolation of obligate anaerobes along with facultative anaerobes in clinical samples received for aerobic culture and sensitivity. There is a need for isolation of these bacteria routinely and a scope for doing antibiotic susceptibility testing, which will help in evidence-based medicine and a better clinical outcome by giving appropriate therapy.

1. Antony B, Justin S, Raveendran R, Shetty AK, Kuruvilla TS, Boloor R. Spectrum of anaerobes encountered in surgical infections in a tertiary care hospital in Mangalore, coastal Karnataka: A prospective study. Muller J Med Sci Res 2016; 7: 40-43.
2. Zhao‐Fleming HH, Wilkinson JE, Larumbe E, Dissanaike S, Rumbaugh K. Obligate anaerobes are abundant in human necrotizing soft tissue infection samples – a metagenomics analysis. APMIS 2019; 127: 577-587.
3. Stone HH, Kolb LD, Geheber CE. Incidence and significance of intraperitoneal anaerobic bacteria. Ann Surg 1975; 181: 705-715.
4. Jousimies-Somer H, Sutter VL, et al (2002). Wadsworth-KTL anaerobic bacteriology manual. 6th. ed. Star Pub. Belmont, CA.
5. Shenoy PA, Vishwanath S, Gawda A, Shetty S, Anegundi R, Varma M, et al. Anaerobic bacteria in clinical specimens - frequent, but a neglected lot: a five year experience at a tertiary care hospital. J Clin Diagn Res 2017; 11: DC44-DC48.
6. Duerden BI. Virulence factors in anaerobes. Clin Infect Dis 1994; 18 Suppl 4: S253-259.
7. Viswanath BG, Lakshmi GJ, Nagamani K, Reddy NVN, Rao GP, Srinivas SSS, et al. Emergence of antimicrobial resistance among anaerobic bacteria. Am J Infect Dis Microbiol 2017; 52: 87-93.
8. Zhao-Fleming H, Dissanaike S, Rumbaugh K. Are anaerobes a major, underappreciated cause of necrotizing infections? Anaerobe 2017; 45: 65-70.
9. Busuttil RW, Davidson RK, Fine M, Tompkins RK. Effect of prophylactic antibiotics in acute nonperforated appendicitis: a prospective, randomized, double-blind clinical study. Ann Surg 1981; 194: 502-509.
10. Kuzaka B, Wróblewska MM, Borkowski T, Kawecki D, Kuzaka P, Młynarczyk G, et al. Fournier’s Gangrene: clinical presentation of 13 cases. Med Sci Monit 2018; 24: 548-555.
11. Viswanathan V, Jasmine JJ, Snehalatha C, Ramachandran A. Prevalence of pathogens in diabetic foot infection in South Indian type 2 diabetic patients. J Assoc Physicians India 2002; 50: 1013-1016.
12. Louie TJ, Bartlett JG, Tally FP, Gorbach SL. Aerobic and anaerobic bacteria in diabetic foot ulcers. Ann Intern Med 1976; 85: 461-463.
13. Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, et al. Co-occurrence of anaerobes in human chronic wounds. Microb Ecol 2019; 77: 808-820.
14. Park Y, Choi JY, Yong D, Lee K, Kim JM. Clinical features and prognostic factors of anaerobic infections: a 7-year retrospective study. Korean J Intern Med 2009; 24: 13-18.
15. Holland JW, Hill EO, Altemeier WA. Numbers and types of anaerobic bacteria isolated from clinical specimens since 1960. J Clin Microbiol 1977; 5: 20-25.
16. Farrokh D, Rezaitalab F, Bakhshoudeh B. Pulmonary actinomycosis with endobronchial involvement: a case report and literature review. Tanaffos 2014; 13: 52-56.
17. Katsenos S, Galinos I, Styliara P, Galanopoulou N, Psathakis K. Primary bronchopulmonary actinomycosis masquerading as lung cancer: apropos of two cases and literature review. Case Rep Infect Dis 2015; 2015: 609637.
18. Gaetti-Jardim EC, Marqueti AC, Faverani LP, Gaetti-Jardim E Jr. Antimicrobial resistance of aerobes and facultative anaerobes isolated from the oral cavity. J Appl Oral Sci 2010; 18: 551-559.
IssueVol 14 No 2 (2022) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v14i2.9179
Obligate anaerobes; Facultative anaerobes; Polymicrobial appearance

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
Ayesha BB, Gachinmath S, Sobia C. Isolation of obligate anaerobes from clinical samples received for routine bacterial culture and sensitivity: a cross sectional study. Iran J Microbiol. 2022;14(2):145-155.