2.3 MIGRACIÓN
2.3.1 Migración Interna
2.3.1.1 Crecimiento poblacional de la capital de San Juan de Tarucani
The RD4 scar and RD9 primers provided sufficient specificity and sensitivity (Chapter 3) for detection of Mb and Mtb respectively. All environmental samples were tested using qPCR with these specific RD probes to quantify the genome number according to a tenfold dilution series from 106 to 1 genome equivalents µl-1 .The prevalence of
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target genome equivalents was compared for samples taken in the wet and dry seasons.
4.3.1.1. Quantification of Mtb and Mb in faecal samples
The 976 faecal samples consisting of 764 cattle and 212 goat samples were examined overall with approximately 60 cattle and 20 goat samples taken from each village. The Mb prevalence in the cattle faeces from different villages indicated high prevalence in both wet and dry season in village 6 which was significantly higher in the wet season but overall counts were higher in the dry season across the majority of villages (Figure 4.4). A similar trend was seen for Mb prevalence in goat faeces with village 6 again showing highest counts in both wet and dry season. The box and whisker plots showed the ranges of Mb genomic equivalents detected from each sample and the outliers represented the most extreme observations including sample maximum or minimum.
The negative skewed distribution of Mb quantification in cattle faecal samples in the dry season was significantly higher (P-value < 0.001) than narrow distribution in the wet season which showed a positive skew (Figure 4.5). However there was no significant difference (P-value > 0.05) in terms of Mb genomic equivalents in goat faeces between two seasons (Figure 4.6).
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Figure 4.4 Comparison of Mb positives (A, B) and quantification of Mb (C, D) in each village over two seasons in the cattle (A, C) and goat faeces (B, D).
Figure 4.5 Mb prevalence in the cattle faeces (A) and ranges (B) over two seasons. ***Mann Whitney test (P-value < 0.001).
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Figure 4.6 Mb prevalence in the goat faeces (A) and ranges (B) over two seasons.
The Mtb from cattle faecal samples in village 1 was highest proportion of any dataset for both cattle and goats across all seasons and all villages with over 50 % positive in the dry season (Figure 4.7). However Mtb in faecal samples in village 5 were significantly high in the wet season because Mtb was rarely detected in faeces (Figure 4.7). There was a pronounced negative skew on the wet season counts for cattle faeces as the dry season counts although with a similar negative skew were approximately 50 % lower (P-value < 0.05) (Figure 4.8).
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Figure 4.7 Comparison of Mtb positive results (A) and quantification of Mtb (B) in each village in the cattle over two seasons. No detection of Mtb in goat faeces.
Figure 4.8 Mtb prevalence in the cattle faeces (A) and ranges (B) over two seasons. *Mann Whitney test (P-value < 0.05).
100 4.3.1.2. Quantification of Mb and Mtb in boma soil samples
There were very few Mb positives in both cattle and goat boma soil and Mb positives only present in village 1 and 6 and only in the wet season (Figure 4.9). No Mb positives from the dry season were detected in any pastoralist villages. The Mb positives ranged between 102 to 104 genomic equivalents g-1 in both cattle and goat soil samples (Figure 4.10 and 4.11).
Mtb was only detected in village 1 in cattle boma soil in the wet season and none was found in the dry season. As for the faeces no Mtb was detected in the goat boma soil (Figure 4.12).
The moisture contained in the boma soil was measured when samples were taken and was significantly higher (P-value < 0.001) in the wet season in both cattle and goat soil samples (Figure 4.13).
Figure 4.9 Comparison of Mb positives (A, B) and quantification of Mb (C, D) in each village over two seasons for cattle (A, C) and goat boma soil (B, D).
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Figure 4.10 Mb prevalence (A) and the range (B) in cattle boma soil over two seasons. No Mb detection in the dry season.
Figure 4.11 Mb prevalence (A) and the range (B) in the goat faeces over two seasons. No Mb detection in the dry season.
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Figure 4.12 Mtb prevalence (A) and quantification (B) in each village over two seasons in cattle boma soil. No Mtb detection in goat boma soil samples.
Figure 4.13 Moisture content in the cattle and goat boma soil over two seasons ***Mann Whitney (P-value < 0.001).
103 4.3.1.3. Quantification of Mb and Mtb in household dust samples
Mb was rarely detected from household dust and detected only village 4 in the dry season (Figure 4.14). Village 5 showed significant prevalence of Mtb in both seasons (Figure 4.15) where positives detected in the wet season reached approximately 106 genomic equivalents g-1 (Figure 4.16).
Figure 4.14 Comparison of Mb positive results (A) and quantification (B) in each village over two seasons in the household dust.
Figure 4.15 Mtb positive results (A) and quantification (B) in each village over two seasons in the household dust samples.
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Figure 4.16 Mtb prevalence in the household dust (A) and the range (B) over two seasons
4.3.1.4. Quantification of Mtb and Mb in water and sediment samples
A high prevalence of Mb was observed in water filters in the wet season (Figure 4.17) as nearly 80 % of water samples contained Mb between 103 to 104 gene copies filter- 1 (Figure 4.18). Nevertheless, Mb species was below qPCR detection in all sediment samples.
The Mtb species was identified in only one sediment sample from eight river locations, Ikwavila (IKW) and Ikonongo (IKO) at approximately 104 Mtb genome equivalents filter-1 (Figure 4.19). However in the filtered water samples Mtb pathogens were under the detection limit for qPCR from water samples in both seasons.
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Figure 4.17 Comparison of Mb positive results (A) and quantification (B) in water filters. No Mb detection in sediment samples.
Figure 4.18 Mb prevalence in the water filters (A) and the range (B) within the two seasons. No Mb detection in the dry season.
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Figure 4.19 Comparison of Mtb positive results (A) and quantification (B) in each river sample location over two seasons in sediment samples. No Mtb detection in water filters.