Southern African Journal of Infectious Diseases Antimicrobial Resistance Surveillance in the South African Private Sector, Report for 2016

Transcription

1 Southern African Journal of Infectious Diseases Antimicrobial Resistance Surveillance in the South African Private Sector, Report for 0 --Manuscript Draft-- Full Title: Manuscript Number: Article Type: Keywords: Abstract: Order of Authors: Antimicrobial Resistance Surveillance in the South African Private Sector, Report for 0 SAJID R1 Original Research Surveillance, antimicrobial susceptibility testing, ESKAPE, resistance Aim. The relevance of surveillance for antimicrobial resistance is increasingly recognised in the light of global action plan to combat resistance. In this report, we present antimicrobial susceptibility testing to ESKAPE pathogens from private sector laboratories in South Africa for 0. Methods. Antimicrobial susceptibility testing (AST) performed on ESKAPE organisms (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) isolated from blood cultures at four private pathology laboratories in 0 were analysed. Analysis and reporting of data were done at uniformed platform created by the NICD for national AST data. Results. We reported AST on 0 ESKAPE organisms including % Enterobacteriaceae, % Gram-positive bacteria and 1% Gram-negative bacteria and we performed drug-bug combination following the Global Antimicrobial Surveillance System (GLASS) guidelines by the World Health Organization. Conclusions. The most important resistance to address is high level of ESBL in Enterobacteriaceae, which impose use of carbapenems for the treatment. Resistance to carbapenems is recorded in this report but not confirmation of genes by genotypic methods. During this period, we have not observed any increase in vancomycin resistant Enterococci. Olga Perovic, MD, MMED, FCPATH Husna Ismail, PhD, MPH Erika van Schalkwyk, MBBCh, MPH Warren Lowman, MBBCh, MMed, FC PATH, Elizabeth Prentice Marthinus Senekal Chetna N Govind Powered by Editorial Manager and ProduXion Manager from Aries Systems Corporation

2 Manuscript - anonymous Antimicrobial Resistance Surveillance in the South African Private Sector, Report for 0 ABSTRACT Aim. The relevance of surveillance for antimicrobial resistance is increasingly recognised in the light of global action plan to combat resistance. In this report, we present antimicrobial susceptibility testing to ESKAPE pathogens from private sector laboratories in South Africa for 0. Methods. Antimicrobial susceptibility testing (AST) performed on ESKAPE organisms (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) isolated from blood cultures at four private pathology laboratories in 0 were analysed. Analysis and reporting of data were done at uniformed platform created by the NICD for national AST data. Results. We reported AST on 0 ESKAPE organisms including % Enterobacteriaceae, % Gram-positive bacteria and 1% Gram-negative bacteria and we performed drug-bug combination following the Global Antimicrobial Surveillance System (GLASS) guidelines by the World Health Organization. Conclusions. The most important resistance to address is high level of ESBL in Enterobacteriaceae, which impose use of carbapenems for the treatment. Resistance to carbapenems is recorded in this report but not confirmation of genes by genotypic methods. During this period, we have not observed any increase in vancomycin resistant Enterococci. INTRODUCTION Over the last 0 years, antimicrobial resistance (AMR) has reached a pandemic level. 1 According to estimates by the U.S. Centres for Disease Control and 1

3 Prevention, each year more than two million people are infected with antimicrobialresistant microorganisms of which,000 people die due to these infections. 1 The Global Report on Surveillance by the World Health Organization indicated that AMR is on the increase in Africa. However, accurate and reliable data are limited, as a result the true extent of the problem is unknown. Here we report on a select group of bacteria that not only cause healthcare-associated infections, but also effectively escape the effects of antimicrobial agents. This group of bacteria is known by the acronym, ESKAPE. The aim of this report was to describe the spectrum of ESKAPE pathogens (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) together with their antimicrobial susceptibility testing (AST) patterns identified from private-sector laboratories across South Africa. METHODS Secondary data analysis was conducted on ESKAPE isolates identified from four accredited private sector pathology laboratories (Ampath, Lancet Laboratories, PathCare and Vermaak and Partners) located in all nine provinces in South Africa, from January to December 0. The study population were all patients who had a blood culture submitted to a private laboratory. We could not distinguish hospitalassociated infections from community-associated infections as admission data were not available at the time of analysis. Positive blood cultures with any one of the ESKAPE organisms isolated were included in the analysis. A 1-day de-duplication rule was applied to all positive blood cultures. AST and interpretation of results were performed according to Clinical and Laboratory Standards Institute (CLSI) 0 guidelines. AST results were categorised based on categorical data, i.e. susceptible (S) and non-susceptible including intermediate (I) and resistant (R). Reporting of susceptibility patterns for drug-bug combinations were performed based on Global Antimicrobial Surveillance System (GLASS) manual. No patient demographic or clinical data were available. AST data for specified ESKAPE isolates were extracted from a secure web-based electronic platform created by the Surveillance Information Management Unit (SIMU) at the National Institute for Communicable Diseases (NICD). These data are available on the AMR dashboard from the NICD website

4 Klebsiella pneumoniae Escherichia coli Acinetobacter baumannii Pseudomonas aeruginosa Enterococcus faecalis Enterococcus faecium Staphylococcus aureus Number of isolates accessible at Absolute frequencies, percentages, bar charts and tables were used to describe the data. RESULTS For the purpose of this report, ESKAPE pathogen profiles were categorised as Enterobacteriaceae (Klebsiella pneumoniae and Escherichia coli), non-fermentative Gram-negative bacteria (Acinetobacter baumannii and Pseudomonas aeruginosa) and Gram-positive bacteria (Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus). Of the 0 blood cultures that grew ESKAPE organisms, % () were Enterobacteriaceae, % (n=) were Gram-positive bacteria and 1% (n=1) were non-fermentative Gram-negative bacteria. Of the seven ESKAPE organisms, Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus were the three organisms most commonly isolated from blood cultures (Figure 1) Figure 1. Number of ESKAPE isolates identified from blood cultures, January to December 0. Enterobacteriaceae 1 Enterobacteriaceae 1 Non-fermentative Gramnegative bacteria 1 Gram-positive bacteria 1

5 Klebsiella pneumoniae Forty-three percent and twenty percent of K. pneumoniae isolates were nonsusceptible to the aminoglycosides: gentamicin and amikacin, respectively. Fortyone percent and twenty-five percent of isolates were non-susceptible to the quinolones: ciprofloxacin and levofloxacin, respectively. Non-susceptibility to the third-generation cephalosporins: cefotaxime/ceftriaxone and ceftazidime were from % to %, while non-susceptibility to the fourth-generation cephalosporin, cefepime was %. Fifty-seven percent of isolates were non-susceptible to the betalactam + beta-lactamase inhibitor, piperacillin/tazobactam. Less than % of isolates were non-susceptible to the carbapenems: imipenem, meropenem and doripenem, but 1% were non-susceptible to ertapenem (Table 1). Escherichia coli Fifteen percent and seven percent of E. coli isolates were non-susceptible to the aminoglycosides: gentamicin and amikacin, respectively. Thirty-one percent and twenty-five percent of isolates were non-susceptible to the quinolones: ciprofloxacin and levofloxacin, respectively. Non-susceptibility to the third-generation cephalosporins, cefotaxime/ceftriaxone and ceftazidime were from % to %, while non-susceptibility to the fourth-generation cephalosporin, cefepime was %. Twenty percent of isolates were non-susceptible to the beta-lactam + beta-lactamase inhibitor, piperacillin/tazobactam. Less than one percent of isolates were nonsusceptible to the carbapenems: imipenem, meropenem, ertapenem and doripenem, respectively (Table 1).

6 Table 1. Antimicrobial susceptibility patterns of Enterobacteriaceae isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Klebsiella pneumoniae complex Escherichia coli Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Amikacin Amoxicillin-clavulanic acid Ampicillin/amoxicillin Cefepime Cefotaxime/ceftriaxone Ceftazidime Ciprofloxacin Cotrimoxazole Doripenem Ertapenem Gentamicin Imipenem Levofloxacin Meropenem Piperacillin/tazobactam Abbreviations: number of isolates (n), percentage (%), not reported (-) Colistin was not reported as no reference method was applied at private-sector laboratories.

7 Non-fermentative Gram-negative bacteria Acinetobacter baumannii Forty-seven percent and thirty-seven percent of A. baumannii isolates were nonsusceptible to the aminoglycosides: gentamicin and amikacin, respectively. Nonsusceptibility to the carbapenems: imipenem and meropenem were from % to %, while non-susceptibility to doripenem was observed in % of the isolates. Susceptibility patterns for tetracycline and minocycline were not reported, however, ten percent of isolates were non-susceptible to tigecycline (Table ). Pseudomonas aeruginosa Less than % of P. aeruginosa isolates were non-susceptible to the thirdgeneration cephalosporin, ceftazidime and the fourth-generation cephalosporin, cefepime. Non-susceptibility to the carbapenems: meropenem and imipenem was % and %, while non-susceptibility to doripenem was observed in % of the isolates. Thirty-six percent of isolates were non-susceptible to the beta-lactam + beta-lactamase inhibitor, piperacillin/tazobactam (Table ).

8 Table. Antimicrobial susceptibility patterns of non-fermenters isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Acinetobacter baumannii Pseudomonas aeruginosa Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Amikacin Cefepime Ceftazidime Doripenem Gentamicin Imipenem Meropenem Piperacillin/tazobactam Tigecycline Abbreviations: number of isolates (n), percentage (%), not reported (-) Colistin was not reported as no reference method was applied at private-sector laboratories.

9 Gram-positive bacteria Enterococcus species Enterococcus faecalis Twenty-five percent of E. faecalis isolates were non-susceptible to penicillin/ampicillin. Less than one percent of isolates was non-susceptible to the glycopeptides: teicoplanin and vancomycin, respectively. Less than one percent of isolates was non-susceptible to the oxazolidinone, linezolid (Table ). Enterococcus faecium A high proportion of E. faecium isolates (%) were non-susceptible to penicillin/ampicillin. Four percent and five percent of isolates were non-susceptible to the glycopeptides: teicoplanin and vancomycin, respectively. Low levels of nonsusceptibility were observed in two percent of isolates to the oxazolidinone, linezolid (Table ). Staphylococcus aureus Twenty-six percent of S. aureus isolates were non-susceptible to cloxacillin and could be classified as methicillin-resistant S. aureus (MRSA) (Table ).

10 Table. Antimicrobial susceptibility patterns of enterococci species isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Enterococcus faecalis Enterococcus faecium Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Daptomycin N/A N/A 0.0 N/A N/A. Linezolid Penicillin/ampicillin Teicoplanin Vancomycin Abbreviations: number of isolates (n), percentage (%) Table. Antimicrobial susceptibility patterns of Staphylococcus aureus isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Staphylococcus aureus Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Cloxacillin Abbreviations: number of isolates (n), percentage (%)

11 DISCUSION Almost the same number of ESKAPE pathogens were isolated from blood cultures in public sector, compared to 0 from private laboratories (unpublished data) in 0. In the private sector % of K. pneumoniae isolates (n=) were resistant to rd and th generation cephalosporins compared to % (n=) in public sector (unpublished data). Of the total number of E. coli isolates (n=1), % showed non-susceptibility to rd and th generation cephalosporins in private sector compared to % of E. coli isolates (n=0) in the public, while % were non-susceptible to ciprofloxacin in both sectors. Regarding non-fermentative Gram-negative bacteria, % of A. baumannii isolates (n=) were non-susceptible to carbapenems in private sector while 0% (n=) in the public sector. P. aeruginosa isolates showed similar susceptibility patterns in both public and private sectors. Gram-positive organisms showed much stable susceptibility patterns and no vancomycin resistant Enterococci outbreaks were noted during this period. MRSA was identified in % of S. aureus isolates (n=) from public and % isolates (n=) in the private sector. LIMITATIONS In this report, not all private laboratories were included (only, the four largest private groups). Another limitation is the different practices employed by private laboratories, which may influence specimen submission practices and the testing and reporting of results. For instance, in this report we observed that for each of the ESKAPE pathogens, the number of isolates tested for the various antimicrobial agents were different. We haven t been able to report on colistin AST due to changed methodology by CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 01. Data in this report only represents a snapshot over one year, thus long term data are required for trend analysis. CONCLUSIONS

12 K. pneumoniae and E. coli remain the commonest blood culture pathogens in the private-sector for 0. More than 0% of K. pneumoniae isolates and more than 1% of E. coli isolates were non-susceptible to the third- and fourth-generation cephalosporins, which is of concern. Carbapenem resistance among nonfermentative Gram-negative bacteria is alarming. Less than 0% of A. baumannii isolates were susceptible to carbapenems. From all P. aeruginosa isolates, % were susceptible to piperacillin/tazobactam. On a positive note, % of E. faecalis isolates were susceptible to penicillin/ampicillin with less than one percent showing non-susceptibility to the glycopeptides. However, as expected, only eight percent of E. faecium isolates were susceptible to penicillin/ampicillin with less than five percent showing non-susceptibility to the glycopeptides. The prevalence of vancomycin resistance was higher among E. faecium isolates compared to E. faecalis isolates. Approximately one quarter of all S. aureus bacteraemia was caused by MRSA. This report represents national data and it should be stressed that local and/or institutional level data should be utilised to help direct empiric treatment guidelines. REFERENCES 1. Akova M. Epidemiology of antimicrobial resistance in bloodstream infections. Virulence, 0; :, -.. World Health Organization [Internet]. Antimicrobial resistance: global report on surveillance, WHO 01 [Updated June 01; cited 0 October 01]. Available from: Pogue JM, Kaye KS, Cohen DA, Marchaim D. Appropriate antimicrobial therapy in the era of multidrug-resistant human pathogens. Clin Microbiol Infect, 01; 1:-.. Performance Standards for Antimicrobial Susceptibility Testing. Clinical and Laboratory Standards Institute (CLSI), 0; M 0-S.. World Health Organization. Global Antimicrobial Resistance Surveillance System: Manual for Early Implementation. WHO 01 ISBN 0

13 DISCLAIMER Data are reported as received through the SIMU. No demographic, epidemiological, clinical or molecular data were available to distinguish between healthcareassociated and community-associated infections. CHARM is not responsible for testing or reporting results at patient level. ACKNOWLEDGEMENTS We wish to thank the following: - Ms Sue Candy and her team at the SIMU for preparing the data - SASCM editorial committee (Prof O. Perovic, Dr W. Lowman, Prof. N. Govender, Dr C. Sriruttan, Dr K. Moodley, Dr C. Govind, Dr I. Zietsman, Dr B. Magazi, Dr R Kularatne, Dr M Maloba, Dr C. Bamford, Dr K. Swe Swe-Han and Dr Y. Mahabeer) for comments and suggestions 1

14 Manuscript - with author details Antimicrobial Resistance Surveillance in the South African Private Sector Report for 0 Olga Perovic 1,, Husna Ismail 1, Erika van Schalkwyk 1, Warren Lowman,, Elizabeth Prentice, Marthinus Senekal, Chetna N Govind Affiliations 1 Centre for Healthcare-Associated Infections (HAIs), Antimicrobial Resistance (AMR) and Mycoses, National Institute for Communicable Diseases, a division in the National Health Laboratory Service Faculty of Health Sciences, School of Pathology, Department of Clinical Microbiology and Infectious Diseases at University of Witwatersrand, Johannesburg Vermaak and Partners/ Pathcare Pathologists, Department of Clinical Microbiology Wits Donald Gordon Medical Centre, Johannesburg Ampath Microbiology National Reference Laboratory, Centurion Pathcare Pathology Group Reference Laboratory, Goodwood Department of Clinical Microbiology, Lancet Laboratories, Durban, KwaZulu-Natal & Honorary Research Fellow, College of Health Sciences, University of KwaZulu- Natal, Durban, South Africa ABSTRACT Aim. The relevance of surveillance for antimicrobial resistance is increasingly recognised in the light of global action plan to combat resistance. In this report, we present antimicrobial susceptibility testing to ESKAPE pathogens from private sector laboratories in South Africa for 0. 1 Formatted: Numbering: Continuous

15 Methods. Antimicrobial susceptibility testing (AST) performed on ESKAPE organisms (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) isolated from blood cultures at four private pathology laboratories in 0 were analysed. Analysis and reporting of data were done at uniformed platform created by the NICD for national AST data. Results. We reported AST on 0 ESKAPE organisms including % Enterobacteriaceae, % Gram-positive bacteria and 1% Gram-negative bacteria and we performed drug-bug combination following the Global Antimicrobial Surveillance System (GLASS) guidelines by the World Health Organization. Conclusions. The most important resistance to address is high level of ESBL in Enterobacteriaceae, which impose use of carbapenems for the treatment. Resistance to carbapenems is recorded in this report but not confirmation of genes by genotypic methods. During this period, we have not observed any increase in vancomycin resistant Enterococci. INTRODUCTION Over the last 0 years, antimicrobial resistance (AMR) has reached a pandemic level.. 1 According to estimates by the U.S. Centres for Disease Control and Prevention, each year more than two million people are infected with antimicrobialresistant microorganisms of which,000 people die due to these infections. 1 The Global Report on Surveillance by the World Health Organization indicated that AMR is on the increase in Africa. However, accurate and reliable data are limited, as a result the true extent of the problem is unknown. Here we report on a select group of bacteria that not only cause healthcare-associated infections, but also effectively

16 escape the effects of antimicrobial agents. This group of bacteria is known by the acronym, ESKAPE. The aim of this report was to describe the spectrum of ESKAPE pathogens (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) together with their antimicrobial susceptibility testing (AST) patterns identified from private-sector laboratories across South Africa. METHODS Secondary data analysis was conducted on ESKAPE isolates identified from four accredited private sector pathology laboratories (Ampath, Lancet Laboratories, PathCare and Vermaak and Partners) located in all nine provinces in South Africa, from January to December 0. The study population were all patients who had a blood culture submitted to a private laboratory. We could not distinguish hospitalassociated infections from community-associated infections as admission data were not available at the time of analysis. Positive blood cultures with any one of the ESKAPE organisms isolated were included in the analysis. A 1-day de-duplication rule was applied to all positive blood cultures. AST and interpretation of results were performed according to Clinical and Laboratory Standards Institute (CLSI) 0 guidelines. AST results were categorised based on categorical data, i.e. susceptible (S) and non-susceptible including intermediate (I) and resistant (R). Reporting of susceptibility patterns for drug-bug combinations were performed based on Global Antimicrobial Surveillance System (GLASS) manual. No patient demographic or clinical data were available. AST data for specified ESKAPE isolates were extracted from a secure web-based electronic platform created by the Surveillance Information Management Unit (SIMU) at the National Institute for Communicable Diseases (NICD). These data are available on the AMR dashboard from the NICD website accessible at Absolute frequencies, percentages, bar charts and tables were used to describe the data. RESULTS

17 Klebsiella pneumoniae Escherichia coli Acinetobacter baumannii Pseudomonas aeruginosa Enterococcus faecalis Enterococcus faecium Staphylococcus aureus Number of isolates For the purpose of this report, ESKAPE pathogen profiles were categorised as Enterobacteriaceae (Klebsiella pneumoniae and Escherichia coli), non-fermentative Gram-negative bacteria (Acinetobacter baumannii and Pseudomonas aeruginosa) and Gram-positive bacteria (Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus). Of the 0 blood cultures that grew ESKAPE organisms, % () were Enterobacteriaceae, % (n=) were Gram-positive bacteria and 1% (n=1) were non-fermentative Gram-negative bacteria. Of the seven ESKAPE organisms, Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus were the three organisms most commonly isolated from blood cultures (Figure 1) Figure 1. Number of ESKAPE isolates identified from blood cultures, January to December 0. Enterobacteriaceae Klebsiella pneumoniae 1 Enterobacteriaceae Forty-three percent and twenty percent of K. pneumoniae isolates were non- susceptible to the aminoglycosides: gentamicin and amikacin, respectively. Forty- 1 Non-fermentative Gramnegative bacteria 1 Gram-positive bacteria 1

18 one percent and twenty-five percent of isolates were non-susceptible to the quinolones: ciprofloxacin and levofloxacin, respectively. Non-susceptibility to the third-generation cephalosporins: cefotaxime/ceftriaxone and ceftazidime were from % to %, while non-susceptibility to the fourth-generation cephalosporin, cefepime was %. Fifty-seven percent of isolates were non-susceptible to the betalactam + beta-lactamase inhibitor, piperacillin/tazobactam. Less than % of isolates were non-susceptible to the carbapenems: imipenem, meropenem and doripenem, but 1% were non-susceptible to ertapenem (Table 1). Escherichia coli Fifteen percent and seven percent of E. coli isolates were non-susceptible to the aminoglycosides: gentamicin and amikacin, respectively. Thirty-one percent and twenty-five percent of isolates were non-susceptible to the quinolones: ciprofloxacin and levofloxacin, respectively. Non-susceptibility to the third-generation cephalosporins, cefotaxime/ceftriaxone and ceftazidime were from % to %, while non-susceptibility to the fourth-generation cephalosporin, cefepime was %. Twenty percent of isolates were non-susceptible to the beta-lactam + beta-lactamase inhibitor, piperacillin/tazobactam. Less than one percent of isolates were nonsusceptible to the carbapenems: imipenem, meropenem, ertapenem and doripenem, respectively (Table 1).

19 Table 1. Antimicrobial susceptibility patterns of Enterobacteriaceae isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Klebsiella pneumoniae complex Escherichia coli Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Amikacin Amoxicillin-clavulanic acid Ampicillin/amoxicillin Cefepime Cefotaxime/ceftriaxone Ceftazidime Ciprofloxacin Cotrimoxazole Doripenem Ertapenem Gentamicin Imipenem Levofloxacin Meropenem Piperacillin/tazobactam Abbreviations: number of isolates (n), percentage (%), not reported (-) Colistin was not reported as no reference method was applied at private-sector laboratories.

20 Non-fermentative Gram-negative bacteria Acinetobacter baumannii Forty-seven percent and thirty-seven percent of A. baumannii isolates were nonsusceptible to the aminoglycosides: gentamicin and amikacin, respectively. Nonsusceptibility to the carbapenems: imipenem and meropenem were from % to %, while non-susceptibility to doripenem was observed in % of the isolates. Susceptibility patterns for tetracycline and minocycline were not reported, however, ten percent of isolates were non-susceptible to tigecycline (Table ). Pseudomonas aeruginosa Less than % of P. aeruginosa isolates were non-susceptible to the thirdgeneration cephalosporin, ceftazidime and the fourth-generation cephalosporin, cefepime. Non-susceptibility to the carbapenems: meropenem and imipenem was % and %, while non-susceptibility to doripenem was observed in % of the isolates. Thirty-six percent of isolates were non-susceptible to the beta-lactam + beta-lactamase inhibitor, piperacillin/tazobactam (Table ).

21 Table. Antimicrobial susceptibility patterns of non-fermenters isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Acinetobacter baumannii Pseudomonas aeruginosa Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Amikacin Cefepime Ceftazidime Doripenem Gentamicin Imipenem Meropenem Piperacillin/tazobactam Tigecycline Abbreviations: number of isolates (n), percentage (%), not reported (-) Colistin was not reported as no reference method was applied at private-sector laboratories.

22 Gram-positive bacteria Enterococcus species Enterococcus faecalis Twenty-five percent of E. faecalis isolates were non-susceptible to penicillin/ampicillin. Less than one percent of isolates was non-susceptible to the glycopeptides: teicoplanin and vancomycin, respectively. Less than one percent of isolates was non-susceptible to the oxazolidinone, linezolid (Table ). Enterococcus faecium A high proportion of E. faecium isolates (%) were non-susceptible to penicillin/ampicillin. Four percent and five percent of isolates were non-susceptible to the glycopeptides: teicoplanin and vancomycin, respectively. Low levels of nonsusceptibility were observed in two percent of isolates to the oxazolidinone, linezolid (Table ). Staphylococcus aureus Twenty-six percent of S. aureus isolates were non-susceptible to cloxacillin and could be classified as methicillin-resistant S. aureus (MRSA) (Table ).

23 Table. Antimicrobial susceptibility patterns of enterococci species isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Enterococcus faecalis Enterococcus faecium Non-susceptible Susceptible Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Number of isolates tested n % n % Daptomycin N/A N/A 0.0 N/A N/A. Linezolid Penicillin/ampicillin Teicoplanin Vancomycin Abbreviations: number of isolates (n), percentage (%) Table. Antimicrobial susceptibility patterns of Staphylococcus aureus isolated from blood cultures reported from four private groups in South Africa, 1 January 0 to December 0. Staphylococcus aureus Non-susceptible Susceptible Antimicrobial agent Number of isolates tested n % n % Cloxacillin Abbreviations: number of isolates (n), percentage (%)

24 DISCUSION Almost the same number of ESKAPE pathogens were isolated from blood cultures in public sector, compared to 0 from private laboratories (unpublished data) in 0. In the private sector % of K. pneumoniae isolates (n=) were resistant to rd and th generation cephalosporins compared to % (n=) in public sector (unpublished data). Of the total number of E. coli isolates (n=1), % showed non-susceptibility to rd and th generation cephalosporins in private sector compared to % of E. coli isolates (n=0) in the public, while % were non-susceptible to ciprofloxacin in both sectors. Regarding non-fermentative Gram-negative bacteria, % of A. baumannii isolates (n=) were non-susceptible to carbapenems in private sector while 0% (n=) in the public sector. P. aeruginosa isolates showed similar susceptibility patterns in both public and private sectors. Gram-positive organisms showed much stable susceptibility patterns and no vancomycin resistant Enterococci outbreaks were noted during this period. MRSA was identified in % of S. aureus isolates (n=) from public and % isolates (n=) in the private sector. LIMITATIONS In this report, not all private laboratories were included (only, the four largest private groups). Another limitation is the different practices employed by private laboratories, which may influence specimen submission practices and the testing and reporting of results. For instance, in this report we observed that for each of the ESKAPE pathogens, the number of isolates tested for the various antimicrobial agents were different. We haven t been able to report on colistin AST due to changed methodology by CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 01. Data in this report only represents a snapshot over one year, thus long term data are required for trend analysis. CONCLUSIONS

25 K. pneumoniae and E. coli remain the commonest blood culture pathogens in the private-sector for 0. More than 0% of K. pneumoniae isolates and more than 1% of E. coli isolates were non-susceptible to the third- and fourth-generation cephalosporins, which is of concern. Carbapenem resistance among nonfermentative Gram-negative bacteria is alarming. Less than 0% of A. baumannii isolates were susceptible to carbapenems. From all P. aeruginosa isolates, % were susceptible to piperacillin/tazobactam. On a positive note, % of E. faecalis isolates were susceptible to penicillin/ampicillin with less than one percent showing non-susceptibility to the glycopeptides. However, as expected, only eight percent of E. faecium isolates were susceptible to penicillin/ampicillin with less than five percent showing non-susceptibility to the glycopeptides. The prevalence of vancomycin resistance was higher among E. faecium isolates compared to E. faecalis isolates. Approximately one quarter of all S. aureus bacteraemia was caused by MRSA. This report represents national data and it should be stressed that local and/or institutional level data should be utilised to help direct empiric treatment guidelines. REFERENCES 1. Akova M. Epidemiology of antimicrobial resistance in bloodstream infections. Virulence, 0; :, -.. World Health Organization [Internet]. Antimicrobial resistance: global report on surveillance, WHO 01 [Updated June 01; cited 0 October 01]. Available from: Pogue JM, Kaye KS, Cohen DA, Marchaim D. Appropriate antimicrobial therapy in the era of multidrug-resistant human pathogens. Clin Microbiol Infect, 01; 1:-.. Performance Standards for Antimicrobial Susceptibility Testing. Clinical and Laboratory Standards Institute (CLSI), 0; M 0-S.. World Health Organization. Global Antimicrobial Resistance Surveillance System: Manual for Early Implementation. WHO 01 ISBN 0 1

26 DISCLAIMER Data are reported as received through the SIMU. No demographic, epidemiological, clinical or molecular data were available to distinguish between healthcareassociated and community-associated infections. CHARM is not responsible for testing or reporting results at patient level. ACKNOWLEDGEMENTS We wish to thank the following: - Ms Sue Candy and her team at the SIMU for preparing the data - SASCM editorial committee (Prof O. Perovic, Dr W. Lowman, Prof. N. Govender, Dr C. Sriruttan, Dr K. Moodley, Dr C. Govind, Dr I. Zietsman, Dr B. Magazi, Dr R Kularatne, Dr M Maloba, Dr C. Bamford, Dr K. Swe Swe-Han and Dr Y. Mahabeer) for comments and suggestions 1

27 Author Bio OMB No and (Rev. 0/1 Approved Through 0//00) BIOGRAPHICAL SKETCH Provide the follow ing information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FIVE PAGES. NAME: Perovic, Olga era COMMONS USER NAME (credential, e.g., agency login): POSITION TITLE: Associate Professor EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) INSTITUTION AND LOCATION DEGREE END DATE FIELD OF STUDY (if applicable) MM/YYYY School of Medicine University of Belgrade, Belgrade MD /1 Medicine School of Medicine, University of Witwatersrand, Master of Medicine MOTH 1/00 Johannesburg, Gauteng (Medical Microbiology) Executive UNISA, Pretoria, Gauteng OTH /01 Development Program (EDP) School of Medicine University of Belgrade, Belgarde Other training 1/ Diploma in Paediatrics School of Medicine University of Belgrade, Belgarde Other training /1 Specialist in Microbiology and Parasitology School of Medicine, University of Witwatersrand, Diploma in Tropical Other training 1/ Johannesburg, Gauteng Medicine & Hygiene School of Medicine, University of Witwatersrand, Johannesburg, Gauteng Fellow 0/000 FC PATH (SA) MICRO A. Personal Statement Antimicrobial resistance for ESKAPE and other bacterial organisms from diagnostic and surveillance aspects remain main focus of my activity as pathologist at NICD since 00. I have introduced Antimicrobial Resistance Laboratory activities in 0 at NICD for ESKAPE pathogens and since then I am principal investigator for LARS-Laboratory Based Antimicrobial Resistance Surveillance program. I am member of Strategic and Technical Advisory Group (STAG) on AMR at WHO since 01, and member of WHO GLASS group since 01. I am member of Ministerial Advisory Committee (MAC) on AMR in South Africa and I was contributing to National Action Plan (NAP) for AMR and Antimicrobial Stewardship Guidelines. In 00, I have taken responsibilities for national and international Proficiency Testing Survey (PTS) Programs for microbiology. I have led the program towards accreditation by South African National Accreditation System (SANAS) for PTS (ISO ). I was principal investigator for WHO/NICD External Quality Assessment Programs. Furthermore, I was PI for PTS program for (1) a global Invasive Bacterial Vaccine Preventable Diseases (IB-VPD) Proficiency Testing Scheme (PTS) in 0-1 and PTS GSK BIO malaria project for vaccine trial. My skills in External Quality Assessment Programs have been recognized and acknowledge by some international bodies such as Ministry of Health Refik Saydam National Public Health Agency from Turkey and others including WHO. As principal pathologist at Johannesburg Hospital Microbiology Laboratory/NHLS, my leadership responsibilities to routine diagnostic procedures, accreditation process for microbiology laboratory, teaching of undergraduate (WITS medical, dental, and pharmacist students), postgraduate students (microbiology, medicine, paediatrics, dermatology, surgery, etc.) technologists and others has been substantial. I did consultations regarding appropriate antimicrobial usage, management of patients with infectious diseases, specimen submission and other infectious disease issues on weakly schedule at

28 Johannesburg Hospital adults (Respiratory, Trauma, Cardiothorasic ICUs and Infection Diseases wards) and paediatric (Neonatal ICU). Additionally, clinical consultations regarding appropriate use of antimicrobial agents extended to other health care facilities. Antimicrobial susceptibility testing methods and their clinical applications has always interested me, so that I initiated new national surveillance at GERMS-SA for Laboratory based Antimicrobial Resistance for nosocomial pathogens in 0. Current research projects are detailed see below, as well as postgraduate supervision activities. B. Positions and Honors Positions and Employment - Intern, The Republic Ministry of Health and Social Policy, and D. Misovic Academic Hospital, at the School of Medicine University of Belgrade,, Belgrade - Medical officer, University Clinical Centre, Belgrade - 1 Registrar in Microbiology, University Clinical Centre, Belgrade 1 - Consulatnt, Emergency Center at University Clinical Centre, Belgrade - Scientist in virology, Lancen Laboratories, Johannesburg Microbiology registrar, South AFrican Institute for Medical Reserch, Johannesburg - 00 Lecturer, University of Witwatersrand, Johannesburg Principal Pathologist, National Health Laboratory Service, Johannesburg Senior Lecturer,, University of the Witwatersrand, Johannesburg 00 - Principal Pathologist and AMR Lead, National Institute for Communicable Diseases at NHLS, Johannesburg 01 - Associate Professor,, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg Other Experience and Professional Memberships Honors C. Contribution to Science Complete List of Published Work in My Bibliography: D. Additional Information: Research Support and/or Scholastic Performance

29 Supplementary Material - for review Authors responses RESPONSES BY AUTHORS Reviewers' comments: Reviewer #1: The data presented is incredibly useful and will certainly contribute to the limited baseline data on the subject. However, a few recommendations must be mentioned: 1. Abstract - too short. This should include brief overview of methods/ results/ discussion. We added full abstract as required.. Results - Pseudomonas susceptibilities: was amikacin or fluoroquinolone AST done? These are common antimicrobials for a common infection and clinicians would benefit from knowing the full profile. Staph aureus susceptibilities: only cloxacillin is presented. Again, a full AST profile would be useful for clinicians who use a broader selection of gram-positive cover. As we used GLASS manual not all antibiotics are required and we haven t requested from laboratory, indicated in methods section. There is no discussion. Results are well-presented but no interpretation of data is evident. I would suggest a brief discussion on some of the main points from the data. Were there any unexpected results? What is the congruity between this data and other comparable local or international data? Some issues definitely warrant a dedicated comment eg. ertapenem nonsusceptibility in Klebsiella data. This is particularly relevant with the CRE outbreaks many hospitals are experiencing. Authors added discussion section