The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel

Figures & data

Figure 1. Trends in laboratory-reported bacterial gastroenteritis incidence and sample positivity rates, 2016–April 2023. The transition (‘jump’) point from culture to PCR-based testing was at 2020. (A) Annual incidence rates. (B) Annual sample positivity rates. P-values were >0.05 for the models.

Table 1. Trends of laboratory-reported bacterial gastroenteritis incidence rates and sample positivity rates, January 2016–April 2023.

Year	Campylobacter, n (%)^1	Salmonella, n (%)^1	Shigella, n (%)^1	Total positive/ samples (%)^1
2016	357 (4.1)	120 (1.3)	354 (4)	831/8768 (9.4)
2017	280 (3.3)	98 (1.1)	88 (1)	466/8326 (5.5)
2018	431 (5.1)	113 (1.3)	137 (1.6)	681/8496 (8)
2019^2	347 (4)	124 (1.5)	208 (2.4)	679/8545 (7.9)
2020 Culture PCR	252 (4.1)	112 (1.8)	67(1.1)	431/6179 (7)
	405 (6.5)	142 (2.3)	155(2.5)	702/5857 (12)
2021 Culture PCR	467 (4.7)	188 (1.9)	22 (0.2)	677/9932 (6.8)
	729 (7.3)	227 (2.2)	76 (0.7)	1032/9615 (10.7)
2022 Culture PCR	466 (4)	190 (1.6)	147 (1.2)	803/11749 (6.8)
	848 (6.8)	242 (1.9)	329 (2.6)	1419/12418 (11.4)
2023^3 Culture PCR	191 (5.2)	40 (1.1)	71 (1.9)	302/3677 (8.2)
	295 (8)	56 (1.5)	133 (3.6)	484/3677 (13.1)

¹ -% from total number of samples; ²-excluding the last week of December 2019; ³-January-April 2023.

Table 2. Pre-analytical and microbiological characteristics of PCR-positive bacterial gastroenteritis cases.

	PCR-positive, culture positive cases (n = 227)	PCR-positive, culture negative cases (n = 115)	p-value
Pathogen, n (%)			<0.001
Campylobacter	155 (63.8)	88 (36.2)
Salmonella	46 (90.2)	5 (9.8)
Shigella	26 (54.2)	22 (45.8)
Days from symptom onset to sample submission, mean (SD)	6.06 (5.52)	7.8 (7.74)	0.019
Days from sample submission to culture, mean (SD)	1.63 (0.96)	2.0 (1.18)	0.003
PCR Ct values, mean (SD)	29.07 (5.61)	30.88 (5.94)	0.007

Each variable was examined regarding its association with culture positivity.

Table 3. Demographic and clinical characteristics of PCR-positive bacterial gastroenteritis cases.

	PCR-positive, culture positive cases (n = 227)	PCR-positive, culture negative cases (n = 115)	p-value
Age (years), mean (SD)	19.88 (22.55)	20.24 (23.83)	0.89
Female gender, n (%)	106 (46.7)	55 (47.8)	0.84
Member of a minority group^1, n (%)	44 (19.38)	21 (18.2)	0.73
Underlying morbidities, n (%)	50 (22)	29 (25)	0.5
Regular pharmaceutical therapy, n (%)	60 (26.4)	34 (29.8)	0.5
Hospitalization within one month, n (%)	7 (3.1)	5 (4.5)	0.54
Gastroenteritis in family members, n (%)	72 (31)	35 (30.4)	0.8
Antimicrobial treatment^2, n (%)	114 (50.2)	61 (53)	0.62
Recent (one month) restaurant dining, n (%)	143 (63)	72 (63.2)	0.966
Mean duration of illness, days (SD)	9.38 (7.73)	11.6 (12.63)	0.047
Fever, n (%)	146 (64.3)	71 (61.7)	0.64
Maximal temperature °C, mean (SD)	39.02 (0.85)	38.88 (0.74)	0.25
Shivering, n (%)	83 (36.6)	36 (31.3)	0.33
Diarrhoea, n (%)	213 (93.8)	109 (94.8)	0.72
Vomiting, n (%)	70 (30.8)	39 (33.9)	0.56
Abdominal pain, n (%)	193 (85)	87 (75.6)	0.034

¹ -member of an ethnic-religious group other than Israeli Jews; ²-missing data.