Serotypes and Antimicrobial Susceptibility of Nasopharyngeal Isolates of Streptococcus pneumoniae from Children Less Than 5 Years Old in Egypt

Figures & data

Figure 1 Algorithm for laboratory testing.

Table 1 Number, % and PCV13 Coverage of the Identified NP Serotypes

Serotypes	Number Typable 186	ST % per Typable SP	Serotypes	Number Typable 186	ST % per Typable SP
1	33	17.7	15B/15C	4	2.2
3	3	1.6	17F	4	2.2
4	4	2.2	18ABC	12	6.5
5	18	9.7	19A	8	4.3
6ABC	24	12.9	19F	20	10.8
7A/7F	3	1.6	21	1	0.5
7C/7B/40	1	0.5	22A/22F	2	1.1
8	2	1.1	23A	2	1.1
9V/9F	5	2.7	23F	4	2.2
9N/9L	2	1.1	25F	1	0.5
10A	2	1.1	33A/35F/37	1	0.5
11A/11D	3	1.6	34	8	4.3
12F/12A	5	2.7	35B	1	0.5
13	2	1.1	38	1	0.5
14	10	5.4
Typable number		186	55.7%
Number covered by PCV-13		144	77.4%
non-typable per total samples		31	9.3%
Number positive for SP		217	65.0%
Number negative for SP		117	35.0%
Total NP samples collected		334	100%

Notes: Serotypes in boldface are those covered by 13-valent pneumococcal conjugate vaccine-13 (PCV-13).

Table 2 Antimicrobial Susceptibility of S. pneumoniae Colonizing the Nasopharynx

Antibiotic	Cultured Isolates (110)
	Number of Sensitive Isolates	% Sensitivity
Ampicillin	36	32.7%
Vancomycin	110	100%
Linezolid	110	100%
Tetracycline	36	32.7%
Clindamycin	80	72.7%
Erythromycin	61	55.5%
Levofloxacin	100	90.9%
Sulfamethoxazole-trimethoprim	50	45.5%
Ceftriaxone	60	54.5%

Table 3 Number, Percentage and PCV13 Coverage of Serotypes of 40 S. pneumoniae from IPD

Serotypes	Specimen	Number of Samples	%
1	Blood	8	20
3	CSF	1	2.5
5	Pleural fluid	3	7.5
6ABC	Blood	6	15
7A/7F	Blood	2	7.5
	CSF	1
7C/7B/40	Blood	1	2.5
9V/9F	CSF	1	2.5
11A/11D	Blood	1	2.5
12F/12A	Blood	1	2.5
13	Blood	1	2.5
14	Blood	1	2.5
15B/15C	Blood	1	2.5
17F	Blood	1	2.5
18ABC	pleural fluid	5	12.5
19A	Blood	1	2.5
19F	CSF	1	2.5
21	Blood	2	5
22F/22A	Blood	1	2.5
23A	Blood	1	2.5
Serotypes covered by PCV-13		30	75%

Note: Serotypes in boldface are those included in PCV-13. Vaccine coverage of IPD serotypes is 75%.

Table 4 Antimicrobial Susceptibility of 19 S. pneumoniae Isolates from 19 IPD

	Pen	Amp	CTX	E	CD	lev	LZD	Van	Tet	SXT
Susceptible Number	15	15	16	15	18	17	19	19	13	14
%	79	79	84.2	78.9	94.7	89.5	100	100	68.4	73.7

Table 5 Detection of Resistance Genes in DNA of 40 S. pneumonia from IPD

	PBP2b	mef	erm
Number Positive	11	30	17
%	27.5	75	42.5

Abbreviations: SP, Streptococcus pneumoniae; ST, serotype; AST, antimicrobial susceptibility testing; NP, nasopharyngeal; MDR, multi-drug resistant; Pen, penicillin; Amp, ampicillin; CTX, cefotaxim; E, erythromycin; CD, clindamycin; LZD, linezolid; Van, vancomycin, Tet, tetracycline; SXT, sulfamethoxazole/trimethoprim; PCVs, pneumococcal conjugate vaccines; IPD, invasive pneumococcal disease.

Table 6 Comparison Between Antimicrobial Susceptibility by Vitek and the Detected Resistant Genes by PCR for the 19 Isolated S. pneumonia

Molecular Detection of Resistant Genes		Vitek (MIC)
		Penicillin		Erythromycin
		(S)	(R)	(S)	(R)
	Positive PBP-2b	15	2	-	-
	Negative PBP-2b	2	0	–	–
	Negative Erythromycin Gene	–	–	15	0
	Positive Erythromycin Gene	–	–	2	2