Antimicrobial susceptibility and molecular species identification of clinical carbapenem-resistant bacteria




Abstract. Inggraini M, Nurfajriah S, Priyanto JA, Ilsan NA. 2021. Antimicrobial susceptibility and molecular species identification of clinical carbapenem-resistant bacteria. Biodiversitas 22: 555-562. Antibiotic is the first option treatment for infectious diseases both in human and animal. However, the excessive usage and misuse of antibiotics have driven antibacterial resistances worldwide and the increasing case of antibiotic resistance leads to limited options for treatment. This study aimed to observe antimicrobial susceptibility and molecular identification of carbapenem-resistant human clinical bacteria. A total of nine isolates in this study were collected in 2020 from a teaching hospital in Indonesia. All isolates were originated from various human clinical specimens, including urine, blood, pus, and sputum. Identification using 16s rRNA-based showed that these isolates were closely related to Klebsiella pneumoniae (1/9), A. baumannii (5/9), Escherichia coli (2/9), and Lysinibacillus fusiformis (1/9). According to minimum inhibitory concentration using Vitek Automated Machine, four isolates of multi-drug resistant (MDR) bacteria were found. In contrast, five of them were categorized as extensively-drug resistant (XDR). Interestingly, all of the XDR isolates belonged to A. baumannii. These isolates were resistant to at least seven different antimicrobial classes. A comparison of partial 16s rRNA showed two E. coli had similar variance. While in A. baumannii isolates, we found one of five isolates had a different variance sequence, which suggests different clonality among this species. This study gives an insight into the prevalence of carbapenem-resistant bacteria with XDR criteria in Indonesia.


Bassetti M, De Waele JJ, Eggimann P, Garnacho-Montero J, Kahlmeter G, Menichetti F, Poulakou G. 2015. Preventive and therapeutic strategies in critically ill patients with highly resistant bacteria. Intensive Care Med 41(5): 776-795.
Bassetti M, Righi E, Carnelutti A, Graziano E, Russo A. 2018. Multidrug-resistant Klebsiella pneumoniae: challenges for treatment, prevention and infection control. Expert Rev Anti Infect Ther 16(10): 749-761.
Clinical and Laboratory Standards Institute. 2018. Performance standards for antimicrobial disk susceptibility tests; approved standard-12th ed. Clinical and Laboratory Standards Institute, Wayne, PA.
Gray AP, Allard R, Pare R, Tannenbaum T, Lefebvre B, Levesque S, Longtin Y. 2016. Management of a hospital outbreak of extensively drug-resistant Acinetobacter baumannii using a multimodal intervention including daily chlorhexidine baths. J Hosp Infect 93(1): 29-34.
Gustawan IW, Amir ISH, Astrawinata DAW. 2014. Gambaran Infeksi Acinetobacter baumannii dan Pola Sensitifitasnya terhadap Antibiotik. Sari Pediatri 16(1): 35-40.
Hawkey PM, Livermore DM. 2012. Carbapenem antibiotics for serious infections. BMJ 344: 1-7.
Higgins PG, Lehmann M, Wisplinghoff H, Seifert H. 2010. gyrB multiplex PCR to differentiate between Acinetobacter calcoaceticus and Acinetobacter genomic species 3. J Clin Microbiol 48(12): 4592-4594.
Katsiari M, Mavroidi A, Platsouka ED, Nikolaou C. 2018. Extensively drug-resistant Acinetobacter baumannii bacteraemia in a multidisciplinary intensive care unit during a 6-year period: Risk factors for fulminant sepsis. J Glob Antimicrob Resist. DOI:10.1016/j.jgar.2018.02.006.
Kuntaman K, Shigemura K, Osawa K, Kitagawa K, Sato K, Yamada N, Shirakawa T. 2018. Occurrence and characterization of carbapenem-resistant Gram-negative bacilli: A collaborative study of antibiotic-resistant bacteria between Indonesia and Japan. Int J Urol 25(11): 966-972.
Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, Monnet DL. 2012. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 18(3): 268-281.
Manchanda V, Sanchaita S, Singh N. 2010. Multidrug resistant acinetobacter. J Glob Infect Dis 2(3): 291-304.
Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64(2): 795-799.
Murugan MS, Sinha DK, Vinodh Kumar OR, Yadav AK, Pruthvishree BS, Vadhana P, Singh BR. 2019. Epidemiology of carbapenem-resistant Escherichia coli and first report of blaVIM carbapenemases gene in calves from India. Epidemiol Infect. DOI:10.1017/S0950268819000463
Nordmann P, Poirel L. 2019. Epidemiology and Diagnostics of Carbapenem Resistance in Gram-negative Bacteria. Clin Infect Dis 69: 521-528.
Peleg AY, Seifert H, Paterson DL. 2008. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 21(3): 538-582.
Piperaki ET, Tzouvelekis LS, Miriagou V, Daikos GL. 2019. Carbapenem-resistant Acinetobacter baumannii: in pursuit of an effective treatment. Clin Microbiol Infect 25(8): 951-957.
Reyes J, Aguilar AC, Caicedo A. 2019. Carbapenem-Resistant Klebsiella pneumoniae: Microbiology Key Points for Clinical Practice. Int J Gen Med 12: 437-446.
Rice LB. 2008. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no Eskape. J Infect Dis 197(8): 1079-1081.
Spellberg B, Rex JH. 2013. The value of single-pathogen antibacterial agents. Nat Rev Drug Discov. DOI:10.1038/nrd3957-c1
Suhartono, S., Hayati, Z., & Mahmuda, M. (2019). Distribution of Staphylococcus haemolyticus as the most dominant species among Staphylococcal infections at the Zainoel Abidin Hospital in Aceh, Indonesia. BIODIVERSITAS 20(7), 2076-2080. doi:10.13057/biodiv/d20073
Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Lynch SV. 2015. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. DOI:10.1371/journal.pone.0117617
Viehman JA, Nguyen MH, Doi Y. 2014. Treatment options for carbapenem-resistant and extensively drug-resistant Acinetobacter baumannii infections. Drugs 74(12): 1315-1333.
Vilacoba E, Almuzara M, Gulone L, Rodriguez R, Pallone E, Bakai R, Ramirez MS. 2013. Outbreak of extensively drug-resistant Acinetobacter baumannii indigo-pigmented strains. J Clin Microbiol 51(11): 3726-3730.
Wenzler E, Kamboj K, Balada-Llasat JM. 2015. Severe Sepsis Secondary to Persistent Lysinibacillus sphaericus, Lysinibacillus fusiformis and Paenibacillus amylolyticus Bacteremia. Int J Infect Dis 35: 93-95.
WHO. 2017. Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics.
Xu L, Sun X, Ma X. 2017. Systematic review and meta-analysis of mortality of patients infected with carbapenem-resistant Klebsiella pneumoniae. Ann Clin Microbiol Antimicrob 16(1): 18.
Zhanel GG, Wiebe R, Dilay L, Thomson K, Rubinstein E, Hoban DJ, Karlowsky JA. 2007. Comparative review of the carbapenems. Drugs 67(7): 1027-1052.