Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

Existence of antibiotic resistance due to extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria is a major global public health problem [1] and has been reported in all regions of the world [2‐7]. Compared to patients infected with beta-lactam susceptible bacteria, patients infected with ESBL-producing gram-negative bacteria put a greater burden on health-care resources and have an increased risk of treatment failure and poor outcomes including death [8, 9]. High-income countries (HICs) have surveillance systems in place to estimate the burden of bacterial infections due to ESBL-producing gram-negative bacteria, and to determine risk factors for acquisition of ESBL-producing gram-negative bacteria as well as the clinical outcomes associated with infection [1, 10‐12]. In Sub-Sahara Africa (SSA), data on ESBL-producing gram-negative bacteria epidemiology and risk factors associated with ESBL-producing gram-negative bacteria infection are scarce. When available, the data mostly originates from hospital-based studies [13‐18]. Several risk factors have been documented to be associated with ESBL-producing gram-negative bacteria acquisition, including previous hospitalization, previous use of antibiotics such as third-generation cephalosporins, hospital overcrowding, bed sharing when hospitalized, and international travel [19‐25].

In 2002, Blomberg et al. reported high proportions of infections due to ESBL-producing gram-negative bacteria at the National Hospital in Dar es Salaam, Tanzania [26]. Since then, other reports have shown an increasing trend of ESBL-producing gram-negative bacteria infections in the same hospital [14, 27‐29]. Similarly, studies conducted at a tertiary hospital in Mwanza, Tanzania have documented an increase in ESBL-producing gram-negative bacteria infections [28, 30, 31]. Like the centers in Dar es Salaam and Mwanza, Kilimanjaro Christian Medical Centre (KCMC) is a major zonal tertiary healthcare facility, serving nearly one quarter of Tanzania’s estimated 53.5 million inhabitants [32]. Its setting however sets KCMC apart: the Kilimanjaro region in Tanzania has among the highest international movements of people in the country for tourism and business. The region has four distinct ecosystems inhabited by diverse communities of miners, pastoralists, agrarians, and fishermen. Given the public health importance of ESBL-producing gram-negative bacteria, the role that KCMC plays in guiding empirical treatment, and the need for therapeutic decisions to be based on guidelines which are derived from local epidemiological data [33], a study on ESBL-producing gram-negative bacteria in KCMC was found to be imperative. In our setting, little attention is paid to gram-negative bacteria, although they have been reported in east Africa and elsewhere to be causes of outbreaks and to be main contributors of ESBL resistance due to production of CTX-M [13, 34]. The aim of this study was to determine the proportion estimates and risk factors for ESBL-producing gram-negative bacteria due to CTX-M using whole genome sequences of all gram-negative bacteria isolated from clinical specimens at KCMC hospital.

This survey investigated the prevalence and possible risk factors for CTX-M gram-negative bacteria in hospitalized patients in Kilimanjaro, Tanzania. It is the first report to investigate ESBL-producing gram-negative bacteria due to CTX-M in clinical specimens using whole genome sequencing and not based on phenotypic testing. To the best of our knowledge, it is the first risk factor analysis of ESBL-producing gram-negative bacteria infections in Tanzania. The overall prevalence of CTX-M gram-negative bacteria in this study was 13.6%. This hospital-study’s findings are comparable with other hospital studies that had previously reported low ESBL-producing gram-negative bacteria prevalence in Gabon, 15.0% [37], and Central Africa Republic, 4 to 19% [38]. However, the report’s prevalence contrasts with 42% prevalence in a review on general ESBL-producing gram-negative bacteria in East Africa hospitals [34], a 29.7% prevalence previously reported in Kilimanjaro by Kajeguka et al. [39], and 32.6% prevalence reported in Guinea-Bissau [22]. Further, our findings contrast with other reports on ESBL-producing gram-negative bacteria in hospitals outside the East African region in that they had shown higher prevalence than in this report: Cameroon 55% [19], Ghana 49% [23], Egypt above 45% [40], and South Africa 83% [41]. There could be several reasons for the observed low prevalence (13.6%) of CTX-M gram-negative bacteria, including the fact that the majority of patients were sampled while they had been on antibiotics for a number of days since admission. The prevalence of CTX-M gram-negative bacteria was observed to decrease with hospitalization days. The use of ceftriaxone in the majority of inpatients at KCMC is a plausible explanation for the observed low prevalence of CTX-M, and the decrease in prevalence over time. Moreover, the prevalence of CTX-M at admission may be relatively high due to selection of ESBL-producing gram-negative bacteria in the community due to overuse of antibiotics other than ceftriaxone. A comparison of CTX-M resistance between patients on ceftriaxone versus patients on other cephalosporins like ceftazidime or cefepime would have been of great interest; however, the available data was insufficient for this analysis.

Prevalence of CTX-M gram-negative bacteria appeared to increase with age. The numbers of patients with age more than 65 years in this study were low, so the comparison with other publications could not be done. Other reports [42‐44] have shown adults over 65 to be almost three times at risk of infection with ESBL-producing gram-negative bacteria. Due to their diminishing immunity and repeated hospitalization, this group is more prone to infections including resistant bacterial strains. However, there appears to be no statistical evidence to support the observed proportion differences in the risks of the CTX-M gram-negative bacteria across age groups.

We investigated whether or not sleeping on stretchers and sleeping in corridors as proxy indicators of overcrowding were associated with the CTX-M gram-negative bacteria. It was found that the prevalence of CTX-M gram-negative bacteria in patients sleeping in ward corridors (on stretchers) as the proper beds were all occupied and no space inside the rooms were relatively high compared to their counterparts. However, sleeping on stretchers and sleeping in corridors were not significantly associated with increased risk of isolating CTX-M gram-negative bacteria.

Factors that showed statistically significant associations with CTX-M gram-negative bacteria include prior admission, currently on antibiotics, use of Ceftriaxone, and wound infections. This report shows that a large proportion (71.9%) of patients was already on antibiotics therapy when specimens were collected for microbiological analyses. Prevalence of isolating CTX-M gram-negative bacteria from patients who were on at least one type of antibiotics was higher (6.8%) than in those who were not (3.7%). The likelihood of isolating CTX-M gram-negative bacteria from those who were currently on antibiotics was found to be four times higher than from those who were not on antibiotics therapy. Reports have shown that the risk of developing antibiotics resistance in societies where antibiotics are excessively used is high [44, 45] due to antimicrobial resistance selection pressure. In KCMC, being a referral hospital, the patients coming to seek medical services are those who might have used antibiotics but treatment failed due to carriage of resistant strains prior to their referrals. Furthermore, given the fact that patients are referred to our hospital from different healthcare facilities, the likelihood of patients to have been on antibiotics is high. Self-referred patients rarely have a paper record of prior medications. Empirical therapy, self-medication, and over-the-counter medications are common in low-income countries (LIC) [46‐48]. This experience-based therapy practiced by physicians in LIC is one of the factors fuelling emergence of resistance, particularly when unnecessarily switching to higher generations of antibiotics.

A substantial proportion (34.5%) of CTX-M gram-negative bacteria was isolated from patients who had a history of admission (hospitalization). The prevalence of isolating CTX-M gram-negative bacteria from patients with no history of admission (hospitalization) was 6.4%, higher than 5.1% in those with hospitalization history. However, the likelihood of isolating CTX-M gram-negative bacteria from patients with history of admission was approximately four times lower than their counterparts, consistent with a recent report [49] that showed a 32% lower risk of ESBL-producing gram-negative bacteria among previously hospitalized patients. It could be that during past admissions, these patients were put on Ceftriaxone doses that had successfully treated CTX-M gram-negative bacteria. This report suggests that Ceftriaxone could be effective against CTX-M gram-negative bacteria. Furthermore, the observed high risk of CTX-M gram-negative bacteria among those who had no prior admission could be explained by the fact that they were carrying resistant CTX-M gram-negative bacteria from the community. However, these findings are different from reports [20, 45, 50, 51] which found that previous admission and use of cephalosporins increase the risk of CTX-M gram-negative bacteria.

A benefit of this study is its contribution to a larger project in which we have been able to build an infrastructure and implement next-generation sequencing (NGS) techniques for clinical diagnostics. For the current report, we have been able to analyze clinical specimens by doing whole genome sequencing to identify CTX-M genes that code for ESBL. We acknowledge that several limitations need to be addressed. Firstly, wound and pus swab specimens make up the majority of samples studied. Microbiology results do not always represent the cause of the infection. Secondly, in this report, ESBL-producing gram-negative bacteria resistance was defined based on the presence of the CTX-M gene. Despite its important role in resistance, this restricted definition means we may have underestimated the ESBL-producing gram-negative bacteria prevalence. Underestimation of ESBL-producing gram-negative bacteria resistance could also be attributed to sampling patients who were already on antibiotics treatment. Thirdly, though our report highlights some key aspects regarding prevalence and risk factors for ESBL-producing gram-negative bacteria resistance due to CTX-M gram-negative bacteria that are important in programming for antimicrobial control, the study was insufficiently powered to confidently draw conclusions about all suspected variables, especially those that appeared contradicting. Fourth, this study was unable to differentiate between community-acquired and hospital-acquired ESBL-producing gram-negative bacteria as clinical sampling was done during, rather than prior to hospitalization. Finally, the widespread use of antibiotics in our settings makes it difficult to ascertain whether or not exposure to antibiotics preceded the emergency of ESBL-producing gram-negative bacteria resistance due to CTX-M.

In conclusion, although the prevalence of ESBL-producing gram-negative bacteria due to CTX-M in this setting was found to be low, it is worthwhile to devise approaches aimed at containing the situation before it gets out of control. To properly stop their spread in the hospital, apart from direct containment methods, we recommend setting up a hospital surveillance system that takes full advantage of the available NGS facility to routinely screen for other resistant bacterial genes.