Carbapenem resistance among uropathogens isolated from Refugees at Nakivale settlement Isingiro district-a cross sectional study

doi:10.21203/rs.3.rs-4658283/v1

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Carbapenem resistance among uropathogens isolated from Refugees at Nakivale settlement Isingiro district-a cross sectional study

https://doi.org/10.21203/rs.3.rs-4658283/v1

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Introduction:

Carbapenem resistant Uropathogens are an ongoing public-health problem globally. This is mediated by transferable Carbapenemase-encoding genes spreading rapidly causing serious outbreaks and dramatically limiting treatment options. Knowledge about the prevalence and factors associated with carbapenem resistant Uropathogens and common carbapenem resistance genes among refugees in Nakivale is limited.

Methods.

We recruited 308 consenting participants in Nakivale refugee settlement in south western Uganda. Quantitative conventional culture on Cysteine Lactose Electrolyte Deficiency (CLED) agar and conventional biochemical tests were used for isolation. The Modified Hodges test was used for phenotypic screening of Carbapenem resistant producing isolates and interpretation made using the Clinical Laboratory Standard Institute guidelines, 2022. DNA was extracted by boiling method and Carbapenemase genes assayed by Gel Electrophoresis. Bivariate and multivariate logistic regression using STATA version14.0 was done to identify the factors associated with Carbapenem resistance producers. Ethical clearance was obtained from MUST-Institutional Review board.

Results.

The overall significant single bacterial growth was 28.8% (89/308). The Phenotypic and genotypic prevalence of Carbapenem resistance was 61.8% (55/89) and 22.5% (20/89) respectively. The commonest isolate was Escherichia coli, 35.5% (32/89) while the most frequent carbapenemase resistant gene was KPC,15% (13/89). Factors associated with Carbapenem resistance were; history of self-medication (OR = 5.09, 95% CI: 1.04–24.77, p < 0.044), antibiotic use before laboratory diagnosis (OR = 6.07, 95% CI: 1.77–20.81, p = 0.004), Having spent more than 5 months on antibiotics (OR = 8.52, 95% CI: 1.47–49.36, p = 0.017).

Conclusion

. The prevalence of Carbapenem resistance among Uropathogens isolated from refugees at Nakivale settlement was high. Accurate antimicrobial stewardship program implementation in refugee settlements are urgently needed. Screening and identification of Carbapenem Resistant Enterobacterial careers among refugees at entry point could be helpful in mitigating spread in refugee settlement.

Urinary tract infection (UTIs) referred to inflammation of urinary tract caused presence and growth of microorganisms[1] and UTIs meant urethritis, cystitis or pyelonephritis [2]. Management of UTIs at Nakivale refugee settlement was largely empirical without urine culture and antibiotic susceptibility testing to guide chemotherapy, a practice that risked antibiotic resistance to cephalosporins, quinolones and carbapenemase among Uropathogens[3].

UTIs was the commonest bacterial infection affecting all age groups and a major cause of hospitalization carbapenem resistance among the refugees [4]. The prevalence of nosocomial and community acquired UTIs associated with carbapenem resistance was 19.8% and 5.4% respectively and caused a 2.3% mortality among gram negative bacteria, this made empirical decisions by clinicians very difficult [5, 6]. Carbapenems are the last choice antibiotics for most MDR organisms and global trend of Carbapenem resistance was exponentially rising due to production of β-lactamases and carbapenemase that hydrolyzed rapidly β-lactam antibiotics of 3rd and 4th generation and carried plasmid encoded genes no longer susceptible to most of antibiotic classes for treatment of UTIs which caused superbug infections[7] [8] especially in vulnerable communities like refugees.

The most prevalent Carbapenem resistant bacteria isolated from refugees were Acinetobacter spp 74.2%, E. coli 8.1%, K. pneumoniae 15.4% respectively[9]. A retrospective study in Germany about dissemination of carbapenem resistant Pseudomonas aeruginosa (PA) and their susceptibilities to ceftolozane-tazobactam (CCT) in Germany showed that 11.2% of nosocomial acquired PA were resistant to meropenem and imipenem but 96.4% susceptible to CCT and this study showed that CCT can be recommended for treatment of resistant PA [10]

To combat antimicrobial resistance, Uganda Clinical Guidelines prohibited use of broad-spectrum antibiotic like 3rd and 4th generation cephalosporins, use of last choice drugs like Carbapenems while it promoted early detection and diagnosis, proper prescriptions and hand hygiene which were not usually followed as recommended by WHO [11]

Diagnosis of UTIs was routinely by use of urine dipstick for raised white blood cell count, esterases and nitrites while urine culture and molecular detection of Carbapenemase and β- lactamase resistant genes in Uganda was limited by fewer capable laboratories [12]. Rudimentary diagnosis of Carbapenem resistant Uropathogens resulted into increased mortality due to treatment failures, recurrence of infections and complicated UTIs among refugees and the general public [13]

Uganda hosted refugees from around the great lakes’ region for over two decades. The continuous influx of unscreened refugees added more burden to already struggling health care in Uganda due to lack and or limited laboratory diagnostic services for detection of carbapenem resistant determining genes among Uropathogens and general antibiotic resistances in refugee camps like Nakivale [14].

Therefore, this study focused on determining the prevalence and factors associated with Carbapenem resistance determining genes isolated among Uropathogens from refugees at Nakivale settlement, Isingiro district

This was a cross sectional study that was carried out in Nakivale refugee settlement. The settlement hosts over 119,587 refugees from the Democratic Republic of Congo, Burundi, Somalia, Rwanda, Ethiopia and Eritrea. Nakivale refugee settlement was officially recognized in 1960 through the Uganda Gazette General Notice No. 19 and is Uganda’s oldest and Africa’s largest refugee settlement and 8th largest settlement in world. It’s was located in south western Uganda Isingiro district approximately 200kms from the capital Kampala and covered over 180 square kilometers of land. Its composed of three administrative zones Base camp, Juru and Rubondo with 74 villages each hosting between 800–1000 people [15]. Social demographically, refugees were given a small piece of land for subsistence farming through refugee self reliance program (RSR). However, flaws were associated with low financial support from office of prime minister in Uganda and competition from native communities for agricultural land and pastoralism[16].

Study Population and sampling methods

The study population were refugees residing in Nakivale refugee settlement Isingiro District. All refugees who presented with signs and symptoms of UTIs like burning sensation, strong and urge to urinate, cloudy urine or bright pink colored urine were included in the study. Participants who were on concurrent antibiotic treatment like chronic bacterial infections like Tuberculosis were excluded from the study.

Simple random sampling was used. Random numbers were generated and given to each participant. This method gave every eligible member of the refugee population an equal chance to be selected to participate in our study.

Sample/ size calculation

By Kish, Leslie. 1965

$$\:\:\:\:\:\:\:\:n=\frac{{z}^{2}\times\:p\times\:q}{{e}^{2}}$$

n = desired sample size, p = proportion (72.3%) level of MRD of K. Pneumoniae in a study done in Uganda [17] z = Standard normal deviates (1.96) at 95% Confidence interval and e = 5% error.

$\:\text{T}\text{h}\text{e}\:\text{d}\text{e}\text{s}\text{i}\text{r}\text{e}\text{d}\:\text{s}\text{a}\text{m}\text{p}\text{l}\text{e}\:\text{s}\text{i}\text{z}\text{e}=308$ Urine samples

Sample collection, handling transportation and storage

We collected midstream urine. Both male and female participants were instructed on urine sample collection. The samples were transported to Mbarara Regional Referral Hospital testing laboratory in cool box containing ice packs at -4 degrees within 2hrs and those to be examined later were kept in the fridge at 2–8 degrees for 24 hours.

Cultures of Urine samples

Conventional methods of CLED, Triple sugar Iron, Citrate, Sulphur Indole and Motility (SIM) and Muller Hinton agar were prepared aseptically. 5µl of Urine sample was picked using a sterile micropipette spread evenly on CLED agar using sterile loop and incubated for 24–72 hours at 37^oc. Read plates for growth of colonies by color, size, shape, hemolysis, Gram stained colonies to distinguish between gram negative from gram positive organisms. Performed biochemical tests on Triple sugar Iron (TSI), SIM Citrate and Indole to confirm the Uropathogens isolated at Clinical Microbiology Laboratory MUST

Phenotypic and genotypic detection of Carbapenem resistant Uropathogens

Modified Hoghes test. We prepared a 0.5 McFarland dilution of K. pneumonea ATCC 13883 in 5ml saline for both positive and negative controls. Spread a lawn of 1:10 dilution Klebsiella pneumoniae on MHA plate and allow to dry for 3 to 5 minutes. Streaked the isolated vertically and placed Antibiotic diffusion discs (Imipnem, Merapenem and Etarpenem) .Incubated for 18–24 hours at 37^oc. Zones of inhibition were measured millimeters and reported as either susceptible (S) or Resistant (R) following Clinical and Laboratory Standards Institute (CLSI) guidelines.

Genotypically, DNA was extracted by boiling method and 80µl of DNA was stored at -20^oC for further use. Real time PCR was used to amplify DNA and optimization, Master Mix was prepared using template, sample, forward and Reverse primers for each of target markers, Gel electrophoresis performed and compared bands of the test were compared against the ladders of the respective genes.

Statistical entry, cleaning and Analysis

We entered the collected into Epi-data version 4.23, cleaned and exported to STATA Version 14 for analysis. Means and standard deviation were reported for continuous variables while frequencies and percentages were reported for categorical variables in a frequency distribution tables. Participants’ characteristics were compared using Chi-Square test.

Univariate and multivariate logistic regression analysis were used to determine the factors significantly associated with Carbapenem resistance determining genes among Uropathogens isolated from Refugees at Nakivale settlement, Isingiro District.

All variables with a p < 0.05 at Univariate analysis were included in the multivariate logistic regression model. Crude and Adjusted odds ratios with their corresponding 95% Confidence Interval were reported. Variables with a p value of less than 0.05 were considered statistically significantly associated with Carbapenem resistance determining genes. Frequencies and percentages were presented using a pie-chart

Quality control

We collected urine samples in sterile containers. Positive and negative Gram stains of S. aureus and Negative E. coli with known ATCC were used. Double checked to ensure quality results. Culture media were incubated overnight to observe for contamination before inoculating patient samples. Molecular quality control was ensured by assaying positive and negative controls along participants samples in duplicates using standard numbered organisms like of Escherichia coli (ATCC 25922), Klebsiella pneumoniae (ATCC 13883), Enterobacter cloacae (ATCC 23355), Proteus mirabilis (ATCC 25933), P. aeruginosa (ATCC 27853), S. aureus (ATCC 29213), and Enterococcus faecalis (ATCC 29212).

Ethical considerations and Dissemination plan

We obtained Ethical clearance from faculty research ethics committee and Institutional Review Board of Mbarara University of Science and Technology, Uganda National council for Science and Technology, Office of the Prime Minister and Authorities managing Nakivale refugee camp. We sought Informed consent from participants and confidentiality was ensured using participant’s initials (or numbers) and not names; all paper based information was locked in a cupboard and electronic data was accessed by password. Our findings were compiled into a report., copies shared with office of Isingiro DHO, Nakivale Medical team, MTI and MUST. A copy of dissertation was put in the University library and manuscript was written for publication in this journal.

Characteristics of the participants. The majority of participants were within the 20-29 years 141(54.8%), the highest proportion were females 175(56.8%), most had not formal education 162 (52.6%) and had more than one child (75.7). came from DRC 169 (54.9%) were Catholics 164(53.3%), had not gone to school 162(52.6%), had more than one child 230 (74.7%) and arrived by buses/Cars 271 (88%) (Table 1)

Table 1: Social demographic characteristics of the respondents

Variable	n (%)	Carbapenem resistance		P-value
Variable	n (%)	Non CP resistant n (%)	CP resistant n (%)	P-value
Age				0.565
<20	25 (8.1)	24 (8.3)	1 (5.0)
20-29	138 (44.8)	130 (45.1)	8 (40.0)
30-39	82 (26.6)	75 (26.0)	7 (35.0)
40-49	41 (13.3)	40 (13.9)	1 (5.0)
50-59	15 (4.9)	13 (4.5)	2 (10.0)
60 and above	7 (2.4)	6 (2.1)	1 (5.0)
Gender				0.444
Male	133 (43.2)	126 (43.8)	7 (35.0)
Female	175(56.8)	162 (56.3)	13 (65.0)
Nationality				0.680
DRC	169 (54.9)	158 (54.9)	11 (55.0)
Rwanda	92(29.9)	84 (29.2)	8 (40.0)
Burundi	37(12.0)	36 (12.5)	1 (5.0)
Ethiopia	2(1.6)	5 (1.7)	0 (0.0)
Others	5(1.6)	5 (1.7)	0 (0.0)
Religion				0.810
Catholics	164(53.3)	154 (53.5)	10 (50.0)
Protestants	61(19.8)	58 (20.1)	3 (15.0)
Islam	67(21.8)	61 (21.2)	6 (30.0)
Others	16(5.2)	15 (5.2)	1 (5.0)
Education
University	3(1.0)	2 (0.7)	1 (5.0)	0.306
vocational training	14(4.6)	13 (4.5)	1 (5.0)
Secondary	129(41,9)	121 (42.0)	8 (40.0)
No school	162(52.0)	152 (52.8)	10 (50.0)
House hold size				0.038
Stay alone	11(3.6)	9 (3.1)	2 (10.0)
No children	8(2.6)	6 (2.1)	2 (10.0)
Less than one child	60(19.5)	55 (19.1)	5 (25.0)
More than one child	229(74.35)	218 (75.7)	11 (55.0)
Transport means				0.001
Foot/Bicycles	13(4.2)	9 (3.1)	3 (15.0)
Cars/ Buses	260(84.4)	254 (88.2)	12 (60.0)
Motor cycles	35(11.4)	25 (6.7)	5 (25.0)

Behavioral characteristics of the respondents

Majority reported practicing self-medication 197(64.0%), did not take all medication 203(65.9%), few followed prescriptions 92(29.9%), did not honor appointment dates 246(79.9%), stopped medication 169(55.0), few shared medicines 142(46.1%), took un-prescribed antibiotics 216(70.1) and took antibiotics before laboratory diagnosis 172(55.8%) (Table 2)

Table 2: Behavioral characteristics of the respondents

Variable	n (%)	Carbapenem resistance		p-value
Variable	n (%)	Non CP resistant n (%)	Non CP resistant n (%)	p-value
Self-medication				0.012*
No	111(36.0)	109 (37.9)	2 (10.0)
Yes	197(64.0)	179 (62.2)	18 (90.0)
Take all medication				0.100
No	203(65.9)	187 (64.9)	16 (80.0)
Yes	105(34.1)	101 (35.1)	4 (20.0)
Follow prescription				0.604
No	216(70.1)	203 (70.5)	13 (65.0)
Yes	92(29.9)	85 (29.5)	7 (35.0)
Appointment keeping				0.086
No	246 (79.9)	233 (80.9)	13 (65.0)
Yes	62 (20.1)	55 (19.1)	7 (35.0)
Stop medication				0.160
Yes	169(54.9)	133 (46.2)	6 (30.0)
No	139(45.1)	155 (53.8)	14 (70.0)
Share medication				0.027*
No	166(53.9)	160 (55.6)	6 (30.0)
Yes	142(46.1)	128 (44.4)	14 (70.0)
Antibiotic use before laboratory diagnosis				0.004*
Yes	136(44.2)	121 (42.0)	15 (75.0)
No	172(55.8)	167 (58.0)	5 (25.0)

Medical characteristics of the participants

Majority had not been hospitalized 265 (86.0%), did not use invasive devices 171(55.5%), commonest comorbidity was Tuberculosis 11(3.6%), only 7 (5.2%) had Major surgery, had history of antibiotic use 188 (61.0%) and most took antibiotics for less than 30 days 188(62.8%) (Table 3).

Table 3: Medical characteristics of the participants

Variable	n (%)	Carbapenem resistance		p-value
Variable	n (%)	Non CP resistant n (%)	CP resistant n (%)	p-value
Hospitalization				0.424
No	265(86.0)	249 (86.5)	16 (80.0)
Yes	43(13.9)	39 (13.5)	4 (20.0)
Invasive device				0.961
No	171(55.5)	160 (55.6)	11 (55.0)
Yes	137 (44.5)	128 (44.4)	9 (45.0)
Surgical procedures				0.158
No	286(92.9)	269 (93.4)	17 (85.0)
Yes	22(7.14)	19 (6.6)	3 (15.0)
Type of surgery				0.128
No surgery	273(88.6)	258 (89.6)	15 (75.0)
Major	123.9)	10 (3.5)	2 (10.0)
Minor	23(7.5)	20 (6.9)	3 (15.0)
History of use of antibiotics				0.023*
No	120(39.0)	117 (40.6)	3 (15.0)
Yes	188(61.0)	171 (59.4)	17 (85.0)
Duration of antibiotics use				0.007*
<30 days	118(62.8)	112 (65.5)	6 (35.3)
2-4 months	61(32.5)	53 (40.0)	8 (47.0)
> 5 months	9(4.8)	6 (3.5)	3 (17.7)

Phenotypic prevalence of Carbapenem resistance

The Phenotypic prevalence of Carbapenem resistance was found to be 55/308 (18%) (Figure 1)

Figure 1: A pie-chart showing phenotypic prevalence of Carbapenem resistance

Genotypic prevalence of Carbapenem resistance

The genotypic prevalence of Carbapenem resistance was 20/308 (6.49%) (table 4).

Table 4: Genotypic prevalence of Carbapenem resistance

Genotypic prevalence	Frequency (n)	Percentage (%)
Non-genotypic Carbapenem resistant	288	93.5
Genotypic Carbapenem resistant	20	6.49
Total	308	100.0

Distribution of isolates

Majority of the were E. coli 35.8%, followed by K. pneumoneae 20.9% and the least was Hafinia spss 2.2% (figure 2)

Figure 2: A bar graph showing distribution of isolates

The most sensitive carbapenem was Meropenem 53(59.6%) and the most resistant was Etarpenem 35 (39.3%)

Distribution of the commonest resistant determining genes among Uropathogens isolated from Refugees at Nakivale settlement, Isingiro District.

The commonest gene expressed was KPC 15 (55.6%) followed by OXA-48 11 (40.7%) and the least was VIM 1 (3.7%) (Figure 3).

Figure 3: A pie chart showing the distribution of the commonest carbapenem resistant genes

Factors associated with Carbapenem resistant determining genes among uropathogens isolated from Refugees at Nakivale settlement, Isingiro District

At multivariate analysis; Participants who had history of self-medication were 5.09 times more likely to experience Carbapenem resistance as compared to those who were not self-medicating (OR=5.09, 95% CI: 1.04-24.77, P<0.05) .Participants who practiced antibiotic use before laboratory diagnosis had 6.07 higher odds of developing Carbapenem resistance as compared to those who didn’t (OR=6.07, 95% CI: 1.77-20.81, P=0.004). Participants who had spent more than 5 months on antibiotics were 8.52 times more likely to experience Carbapenem resistance as compared to those who had spent less than 1 month (OR=8.52, 95% CI: 1.47-49.36, P=0.017) (table 5)

Table 5: Multivariate analysis of the factors associated with Carbapenem resistance genes

Variable	CP resistant n (%)	cOR (95%CI)	P value	aOR (95%CI)	P-value
Duration of antibiotics use
<30 days	6 (35.3)	Ref.		Ref
2-4 months	8 (47.0)	2.81 (0.93-8.53)	0.067	3.10 (0.95-10.03)	0.059
> 4months	3 (17.7)	9.33 (1.86-46.7)	0.007*	8.52 (1.47-49.36)	0.017**
Self-medication
No	2 (10.0)	Ref.		Ref
Yes	18 (90.0)	5.48 (1.24-24.07))	0.024*	5.09 (1.04-24.77)	0.044**
Shared medication
No	6 (30.0)	Ref.		Ref.
Yes	14 (70.0)	2.91 (1.09-7.80)	0.033*	1.73 (0.56-5.36)	0.340
Antibiotic use before diagnosis
Yes	15 (75.0)	4.14 (1.46-11.70)	0.007*	6.07 (1.77-20.81)	0.004**
No	5 (25.0)	Ref.		Ref.
CP- Carbapenem producers cOR-Crude Odds Ratio aOR-Adjusted Odds Ratio CI-Confidence interval

In this study, the phenotypic prevalence of Carbapenem resistance was 55 (17.8%). These findings are slightly higher than the study done in Canada which found out that CRE was 13.0% associated mainly due to nosocomial infection because no patient reported seeking healthcare abroad or travelled to high Carbapenem resistance endemic areas [18] . Our findings were also slightly higher than those found in Iraq 12.4% and lower than other Middle East and North African Countries like Lebanon 64.5%, Jordan 52.5%, Palestine 47.6% and Israel 30%. These findings in these middle eastern countries are explained by comparable regional culture of liberal antibiotic prescription and the difference could be due to different methods used in this retrospective study compared to modified Hodges method used in our study[19]. Other findings in this region associated carbapenem resistance to genetic modification of gram negative Enterobacteriaceae causing increased expression of antimicrobial inactivating enzymes, decreased permeability [20] and the political unrest in the last decade that created many refugees and broken healthcare systems in these areas was associated with spread of carbapenem resistance bacteria in other parts of the world [19]

However, our findings were lower than what was report in studies carried out in Italy (28.4%) and Spain (37%) [18]. The higher prevalence as compared to what we found in our study could be because Kohler et al’s. study was a 10 year review study which used over 16,804 samples from 9,940 patients in Switzerland while our study was carried out for only three (03) month with only 308 samples. A study done in United Sates of America which showed that 51.4% CRO of the patient suffering from UTIs was associated with empiric treatment[21] Conversely Lower prevalence of CRO was reported in Switzerland (0.3%), Israel (12%), North Lebanon 1.7% [22] attributed to continuous surveillance and diagnostic services in Europe that were lacking at Nakivale refugee camp although other European countries

In this study the genotypic prevalence of Carbapenem resistance was 20 (6.49%). This demonstrated that some of our participants in Nakivale were infected with bacteria which could have under gone plasmid Ampcs ESBL transfer genes or porin mutations. However, our results were much lower than the findings in the study done on Klebsiella pneumoniae 43.1% capsular tying and lower than 22.8% genotypic prevalence of E. coli in tertiary hospitals in Uganda[23] although these studies focused on a single isolate and used Multiplex PCR more sensitive than Gel electrophoresis.

Distribution of the resistant genes

The majority of genes assessed were KPC 15 (55.6%), OXA-48 15(40.7%) and the least was VIM (3.7%). The distribution of our study was affected by the distribution of gram negative bacilli isolates where E.coli and Klebsiella pneumoneae expressed these genes. We did not do sequencing for these genes and therefore we could not adequately describe this distribution.

A study done in ICU unit at Imam Khomeini hospital in Iran reported that 16.66% blaOxa – 48 lower than 40.7% in our study while blaVIM, blaKPC and blaIMP were not detected. The difference could be explained by the fact that this study was done in a hospital setting in ICU unit where infection control was being practiced unlike in Nakivale where people interacted randomly possibly causing the spread of carbapenem resistant Uropathogens ([24]. A clinical study conducted in Canada showed that CPE increased by 0.33/100,000 population despite most of the patience having no history of travel to high endemic areas implying that nosocomial transmission was the likely source of transmission of CRE and the distribution of carbapenemases was VIM (67%), KPC (55%) and New Delhi β- Lactamase (22%) was higher than findings of our study [18]

A study United Kingdom found that water reservoirs contaminated with IMP, KPC and VIM possessing Enterobacteriaceae around hospital premises were major risk factors to CRE causing nosocomial infections among terminally ill and immuno-compromised patients [25]. Although we isolated CPO from urine only, refugees collected water from very few centralized waters taps and bore holes which were being shared with local indigenous population that potentially increased the risk of carbapenem transmission.

Variation in gene distributions like KPC 55.6%, OXA-48 140.7% and the least was VIM 3.7% was an indicator of crossover of genes due to mutations and possession of porin pores which was were the likely risk factors to multidrug and Carbapenem resistance in Nakivale refugee settlement. This was KPC-1 and KPC-2 and KPC-3 and resistance to β-lactams except that a few strains susceptible to tigecycline and ceftazidime/avibactam were carbapenem resistant [26]. Also the emergency of variant ST131 Escherichia coli and blaOXA-244 caused carbapenem resistance eminent [27]. Studies showed that some unique organisms like P.mirabilis wereresistant to tetracycline and polymyxin, colistin due to swarming ability and acquisition of virulent factors because of possession of ESBL bla_CTX-M-15, bla_OXA-48-like genes and possession of integrons through mutations [28] and blaVIM-1[29]. However, we did not do virulent profiles of the isolates identified and we could not exactly determine which factors were responsible for carbapenem resistance among refugees in Nakivale refugee settlement.

In this study, participants who reported use of antibiotic before laboratory diagnosis had 5.9 higher odds of developing Carbapenem resistance compared to those who had no history of use of antibiotics. Most of the participants reported taking medicines empirically to alleviate pain due to UTIs. This was accelerated by lack of advanced microbiology laboratory capable of culture and sensitivity for a long time while in the camp and constantly falling ill for similar infections. Similarly, a study carried out in Indonesia and Japan found that 54.5% of patients who experienced Carbapenem resistance were terminally ill and most of them reported prior use of antibiotics before diagnosis experienced poor Carbapenem resistance [30].

In this study, participants who practiced self-medication were 6.1 times more likely to develop Carbapenem resistance compared to those who were not self-medicating. This could be explained by delays of medical supplies to Nakivale refugee camp that resulted into antibiotic selection pressure and lack of strict regulatory measures in Nakivale Refugee settlement to combat Carbapenem resistance. This phenomenon was reported in Saudi Arabia due to lack regulatory measures in taking prescriptional drugs [31]. Likewise, one study explained that people who self-medicated to alleviate infection symptoms ended up developing antibiotic resistance[32]

In this study, participants who had spent more than 5-months antibiotics were 10 times more likely to develop Carbapenem resistance as compared to those who had spent less than 1 month. Similarly, a study in United States of America (USA) reported that Carbapenem resistance resulted from prolonged use of antibiotics due to over hospitalization [33]. These findings were similar despite the fact that some studies were done in hospital settings and carried out for varied duration of time with a larger sample sizes that may not be adequately compared to our settings in Nakivale Refugee Settlement. Length of hospitalization was associated with carbapenem resistance.

The phenotypic and genotypic prevalence of CR was high. The commonest isolate was E.coli followed by KP. This study found that KPC followed by OXA-48 and the least was VIM. The factors indecently associated CR were; history of self-medication antibiotic use before laboratory diagnosis, spending more than 5 months on antibiotics use. Improving laboratory diagnostic services like culture and sensitivity and point of care equipment in Nakivale refugee settlement and other refugee camps in Uganda is a strategy to stop the spreading and transmission of Carbapenem and other antibiotic resistance in vulnerable communities in Uganda.

Health care workers should screen for antibiotic resistance among refugees from the time of arrival to curb down antibiotic resistance in refugee camps and the surrounding communities. The office of the prime minister, Ministry of Health should promote health education programs about antibiotic resistance and its dangers.

AST

Antimicrobial Susceptibility Testing

AMR

Antimicrobial Resistance

CLSI

Clinical and Laboratory Standards Institute

CRE

Carbapenem Resistance Enterobacteriaceae

CPO

Carbapenem Resistant Organisms

MDR

Multidrug Resistance

PCR

Polymerase Chain Reaction

Ethics approval and consent to participate: The study received ethical clearance from Mbarara University of Science and Technology research and ethics committee (IRB NUMBER: MUST-2022-466).

Consent for publication: We sought Informed consent from participants and confidentiality was ensured using participant’s initials (or numbers) and not names; all paper based information was locked in a cupboard and electronic data was accessed by password. All protocols followed the relevant guidelines and regulations.

Availability of data and materials: Raw data, data set and do file are available and no any other materials are available

Competing Interests: No authors declared any form of interest in this data

Funding: Funding was solely done by the Principle investigator

Author’s contribution

Kabera: Michael: Principal investigator

Calvin Cherop- Statistician for data analysis

Galimaka Wilson– Guided in literature review

Bagenda Charles - Statistician for data analysis

Okongo Benson – Guided in discussion of results

Kennedy Kasaza– Internal supervisor

Ampaire Lucas- Supervisor and correspondent author

Conceptualization- Kabera Michael, Ampaire Lucas and Galimaka Wilson

Acknowledgement:I would like to acknowledge Mr. Mwesigye James of Mbarara Regional Referral Hospital Clinical Microbiology and Emmanuel Niyibikora Medical Teams International Nakivale Refugee Camp for guiding during cultures and quality control and Dr. Joel Bazira of DC laboratories Mbarara for his guidance in DNA extraction and gel electrophoresis

MD TEF. Urinary Tract Infection—Requiem for a Heavyweight. J Am Geriatr Soc. 2017;65(8):1650–5.
Funicane T. Urinary Tract Infection Requiem for a Heavyweight. J Am Geriatr Soc. 2017;65(8):1650–5.
Bahati Johnson BMS, Joseph N, Asiphas O. Kayondo Musa & Kabanda Taseera, Prevalence and bacteriology of culture-positive urinary tract infection among pregnant women with suspected urinary tract infection at Mbarara regional referral hospital, South-Western Uganda. BMC Pregnancy and Childbirth; 2021.
Hossain A et al. Age and gender-specific antibiotic resistance patterns among Bangladeshi patients with urinary tract infection caused by Escherichia coli. Heliyon, 2020. 6(6).
Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in gram-negative bacteria. Clin Infect Dis. 2019;69(Supplement7):S521–8.
Zilberberg MD, et al. Development and validation of a bedside instrument to predict carbapenem resistance among gram-negative pathogens in complicated urinary tract infections. Infect Control Hosp Epidemiol. 2018;39(9):1112–4.
Taz K, Jobayer M, Shamsuzzaman S. Nasal Colonization of Methicillin Resistant Staphylococcus aureus among Healthcare Providers in a Tertiary Care Hospital, Bangladesh. Volume 28. Mymensingh medical journal: MMJ; 2019. pp. 627–33. 3.
Nataraj BH, Mallappa RH. Antibiotic resistance crisis: an update on antagonistic interactions between probiotics and methicillin-resistant Staphylococcus aureus (MRSA). Curr Microbiol. 2021;78(6):2194–211.
Truppa C, Abo-Shehada MN. Antimicrobial resistance among GLASS pathogens in conflict and non-conflict affected settings in the Middle East: a systematic review. BMC Infect Dis. 2020;20:1–26.
Kresken M, et al. Dissemination of carbapenem-resistant Pseudomonas aeruginosa isolates and their susceptibilities to ceftolozane-tazobactam in Germany. Int J Antimicrob Agents. 2020;55(6):105959.
Organization WH. WHO country cooperation strategy 2016–2020: Uganda. 2016.
Oyaert M, et al. Laboratory diagnosis of urinary tract infections: Towards a BILULU consensus guideline. J Microbiol Methods. 2018;146:92–9.
Masajtis-Zagajewska A, Nowicki M. New markers of urinary tract infection. Clin Chim Acta. 2017;471:286–91.
Okoh KE. Detection of Carbapenem-Resistance Genes in Klebsiella Species Recovered from Selected Environmental Niches in the Eastern Cape Province, South Africa. Open access. 2020;9(7):425.
UNHCR. Uganda - Nakivale Settlement Profile, July 2020. Operational data portal refugee situations; 2020.
Svedberg E. Refugee Self-Reliance in Nakivale Refugee, Uganda SIT Graduate Institute/SIT Study Abroad, 2014: p. 1778.
Turugurwa J, et al. Antimicrobial resistance patterns and molecular characterization of Klebsiella pneumoniae in clinical isolates at mbarara regional referral hospital. Adv Infect Dis. 2019;9(03):197.
Kohler PP, et al. Emergence of carbapenemase-producing Enterobacteriaceae, south-central Ontario, Canada. Emerg Infect Dis. 2018;24(9):1674.
Touati A, Mairi A. Epidemiology of carbapenemase-producing Enterobacterales in the Middle East: a systematic review. Expert Rev Anti-infective Therapy. 2020;18(3):241–50.
Moghnieh RA, et al. Phenotypic and genotypic characterisation of cephalosporin-, carbapenem-and colistin-resistant Gram-negative bacterial pathogens in Lebanon, Jordan and Iraq. J global Antimicrob Resist. 2021;27:175–99.
Zilberberg MD, et al. Carbapenem resistance, inappropriate empiric treatment and outcomes among patients hospitalized with Enterobacteriaceae urinary tract infection, pneumonia and sepsis. BMC Infect Dis. 2017;17:1–13.
Hawkey PM, et al. Treatment of infections caused by multidrug-resistant gram-negative bacteria: Report of the British society for antimicrobial chemotherapy/healthcare infection society/british infection association joint working party. J Antimicrob Chemother. 2018;73(suppl3):iii2–78.
Wampande K. Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda. Eur J Biology Biotechnol, 2021. 2(2).
Marzieh Hashemian HK, Kaviar VH, Karamolahi S. Ali Nazari,Mohammad Reza Bagheri, Nourkhoda Sadeghifard & Saeed Khoshnood Mohammad Reza Bagheri, Nourkhoda Sadeghifard & Saeed Khoshnood, Nosocomial infections and antimicrobial susceptibility patterns among patients admitted to intensive care unit of Imam Khomeini hospital in Ilam, Iran. Molecular biology reports, 2023: pp. 5565–5574.
Kizny Gordon AE, et al. The hospital water environment as a reservoir for carbapenem-resistant organisms causing hospital-acquired infections—a systematic review of the literature. Clin Infect Dis. 2017;64(10):1435–44.
Shu L-b et al. Prevalence and phenotypic characterization of carbapenem-resistant Klebsiella pneumoniae strains recovered from sputum and fecal samples of ICU patients in Zhejiang Province, China. Infection and drug resistance, 2018: pp. 11–18.
Welker S, et al. Emergence of carbapenem-resistant ST131 Escherichia coli carrying bla OXA-244 in Germany, 2019 to 2020. Eurosurveillance. 2020;25(46):2001815.
Fursova NK, et al. The spread of bla OXA-48 and bla OXA-244 carbapenemase genes among Klebsiella pneumoniae, Proteus mirabilis and Enterobacter spp. isolated in Moscow, Russia. Ann Clin Microbiol Antimicrob. 2015;14:1–9.
Bontron S, et al. Increased resistance to carbapenems in Proteus mirabilis mediated by amplification of the bla VIM-1-carrying and IS 26-associated class 1 Integron. Microb Drug Resist. 2019;25(5):663–7.
Kuntaman Kuntaman KS, Osawa K, Kitagawa K, Sato K, Yamada N, Nishimoto K, Yamamichi F, Rahardjo D. Usman Hadi, Ni Made Mertaniasih, Shohiro Kinoshita, Masato Fujisawa, Toshiro Shirakawa, Occurrence and characterization of carbapenem-resistant Gram-negative bacilli: A collaborative study of antibiotic-resistant bacteria between Indonesia and Japan. Int J Urol, 2018. 25(11).
Lum EP, et al. Australian consumer perspectives, attitudes and behaviours on antibiotic use and antibiotic resistance: a qualitative study with implications for public health policy and practice. BMC Public Health. 2017;17:1–12.
Haque M et al. Self-medication of antibiotics: investigating practice among university students at the Malaysian National Defence University. Infection and drug resistance, 2019: pp. 1333–1351.
Slayton RB, et al. Vital signs: estimated effects of a coordinated approach for action to reduce antibiotic-resistant infections in health care facilities—United States. Elsevier; 2015. pp. 3002–7.

No competing interests reported.

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Carbapenem resistance among uropathogens isolated from Refugees at Nakivale settlement Isingiro district-a cross sectional study

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Version 1

Abstract

Introduction:

Methods.

Results.

Conclusion

Figures

Introduction

Materials and Methods

Study Population and sampling methods

Sample/ size calculation

Sample collection, handling transportation and storage

Cultures of Urine samples

Phenotypic and genotypic detection of Carbapenem resistant Uropathogens

Statistical entry, cleaning and Analysis

Quality control

Ethical considerations and Dissemination plan

RESULTS

Phenotypic prevalence of Carbapenem resistance

Genotypic prevalence of Carbapenem resistance

Distribution of isolates

Distribution of the commonest resistant determining genes among Uropathogens isolated from Refugees at Nakivale settlement, Isingiro District.

Factors associated with Carbapenem resistant determining genes among uropathogens isolated from Refugees at Nakivale settlement, Isingiro District

DISCUSION OF THE FINDINGS

Distribution of the resistant genes

CONCLUSION AND RECOMMENDATIONS

Abbreviations

Declarations

References

Additional Declarations

Status:

Version 1