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Table 3 Co-infecting organisms and resistance profiles

From: Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019–June 2021)

Organism

Number

Proportion Resistant

Resistance Phenotype

Gram-positives

Staphylococcus aureus

2

0 (0%)

Methicillin-sensitive Staphylococcus aureus (MSSA)

104

0 (0%)

Methicillin-resistant Staphylococcus aureus (MRSA)

132

132 (100%)

Methicillin resistance

Coagulase-negative staphylococci (CNS)

99

30

Unknown resistance (24)

Vancomycin-resistant enterococci (VRE), unspecified

4

4 (100%)

Vancomycin resistance

Enterococcus faecalis

29

1 (3%)

High-level aminoglycoside resistance

Enterococcus faecium

33

6 (18%)

Vancomycin resistance (3); high-level aminoglycoside resistance (3), ampicillin resistance (1)

Enterococcus casseliflavus/Enterococcus gallinarum

2

1 (50%)*

Vancomycin resistance (1 – E. gallinarum)*

Enterococcus spp.

12

0 (0%)

Streptococcus pneumoniae

15

3 (20%)

Amoxicillin, amoxicillin/clavulanic acid, cefoxitin, gentamicin, erythromycin, clindamycin, piperacillin/tazobactam, trimethoprim/sulfamethoxazole (2); amikacin, ciprofloxacin, levofloxacin, cefotaxime, ceftriaxone, ceftazidime, cefepime (1), unknown resistance (1)

Streptococcus spp.

4

0 (0%)

Clostridium difficile

7

0 (0%)

Gram-negatives

   

Acinetobacter baumannii

218

148 (68%)

Wide-spread resistance except to colistin (98); 26 isolates harbored OXA-23, 2 harbored NDM; Carbapenem resistance (4); extensively resistant (5), pan-drug resistant (3), unknown resistance (19)

Klebsiella pneumoniae

274

169 (62%)

26 (carbapenem-producing KPC), OXA-48 (7), ESBL (13), NDM (1), multi-drug resistant (23), Carbapenem resistance (13), KPC-2 (1), KPC-3 (1), unknown resistance (25), VIM (1)

Klebsiella oxytoca

5

2 (40%)

ESBL (2)

Klebsiella aerogenes

4

0 (0%)

Klebsiella spp.

9

0 (0%)

Pseudomonas spp.

4

0 (0%)

Pseudomonas aeruginosa

203

65 (25%)

Unknown resistance (34), piperacillin/tazobactam (4), carbapenems (18), MDR (6), cephalosporin resistance (1), XDR (1)

Serratia marcescens

18

17 (94%)

Resistance to amoxicillin, amoxicillin/-clavulanic acid, 1st and 2nd generation cephalosporins (including AmpC B-lactamase) with low level of resistance to amikacin, multi-drug resistant (7)

Escherichia coli

118

43 (36%)

ESBL (2), AmpC resistance (1), multi-drug resistant (12), unknown resistance (18)

Stenotrophomonas maltophilia

60

24 (40%)

Multidrug resistant (24)

Proteus mirabilis

5

0 (0%)

Proteus putida

1

0 (0%)

Haemophilus influenzae

7

0 (0%)

Moraxella catarrhalis

1

0 (0%)

Enterobacteriaceae, unspecified

5

0 (0%)

Yersinia enterocolitica

1

1 (100%)

Amoxicillin and amoxicillin/-clavulanic acid resistance

Enterobacter spp.

8

5 (63%)

Imipenem resistance

Enterobacter aerogenes

8

8 (100%)

Carbapenem-resistant Enterobacteriaceae (1), ESBL (1), AmpC B lactamase (6), unknown resistance (1)

Enterobacter cloacae

68

29 (43%)

AmpC B lactamase (7), multi-drug resistant (18), NDM-1 (2)

Elizabethkingia meningoseptica

1

1 (100%)

Multi-drug resistant (1)

Chryseobacterium gleum

1

1 (100%)

Multi-drug resistant (1)

Citrobacter koseri

1

0 (0%)

Mycoplasma pneumoniae

2

0 (0%)

Enterobacterales

113

34 (30%)

Cephalosporin resistance (2); Carbapenem resistance (3), unknown resistance (29)

Bacteroides fragilis

2

0 (0%)

Viral organisms

Metapneumovirus

1

0 (0%)

Fungal organisms

Candida auris

11

10 (91%)

Fluconazole resistance (10), Voriconazole non-susceptible (3); overall 3 multi-azole resistant (fluconazole + voriconazole), 7 multi-drug resistant including 3 to 3 classes of drugs (azoles, amphotericin B and 5-flucytosine) and 4 resistant to 2 classes of drugs (azoles + 5-flucytosine and azoles + amphotericin B)

Candida albicans

88

3 (3%)

Fluconazole and voriconazole resistance (3); caspofungin intermediate (2)

Candida dubliniensis

6

2 (33%)

Fluconazole resistance (1), caspofungin resistance (1)

Candida parapsilosis

25

1 (4%)

Fluconazole resistance

Candida glabrata

15

1 (7%)

Pan-echinocandin resistance (1), caspofungin intermediate (7)

Candida spp.

22

5 (23%)

Azole resistance (5); Echinocandin resistance (1)

Pichia kudriavzevii

1

1 (100%)

Caspofungin and fluconazole resistance

Aspergillus fumigatus

3

0 (0%)

Aspergillus flavus

7

0 (0%)

Aspergillus niger

2

0 (0%)

Other

73

20 (27%)

Unknown resistance (9), ESBL (11)

  1. *Intrinsic resistance