Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019–2020. Results of the Invifar network

Introduction

Bacterial species are developing resistance to many antibiotics (Prestinaci, Pezzotti & Pantosti, 2015; Paphitou, 2013; Karam & Heffner, 2000; Laxminarayan et al., 2013; Pogue et al., 2015). To control the dissemination of these organisms, it is necessary to monitor the antimicrobial susceptibility of the microorganisms most frequently detected in hospitals (Roca et al., 2015). The analysis of sterile fluids is essential because potential pathogens are considered significant in most cases (Opota et al., 2015). Blood, cerebrospinal fluid (CSF), and pleural fluid are sterile fluids frequently received in the microbiology laboratory for culture in suspected infections. These infections are associated with considerable morbidity and mortality (Proulx et al., 2005).

Regarding blood cultures, mortality associated with bloodstream infections is directly related to the delay in administering the first adequate antimicrobial agent (Ferrer et al., 2014). Empirical antimicrobial infectious treatments are chosen based on clinical and epidemiological data (Paul et al., 2010).

Bacterial meningitis occurs primarily in childhood and is associated with a high mortality rate and potentially severe morbidity. Antibiotic resistance may limit the effectiveness of treatment (Kim, 2010; Briand et al., 2016). Thus, early diagnosis and appropriate antibiotic therapy are needed to avoid further complications.

Pleural infections are a significant cause of morbidity or death, and their incidence continues to rise (Farjah et al., 2007). Current guidelines recommend pleural fluid microbiological studies to direct antibiotic treatment (Light, 1999). Mortality has been found to increase as much as 40% when gram-negative bacteria, Staphylococcus aureus, or a mixed aerobic infection are detected (Maskell et al., 2006). Thus, reliable identification of these groups would allow the targeting of early aggressive therapy, and calculations of resistance percentages may help in the use of adequate empirical treatments.

It is necessary to define local and national resistance rates for various pathogens in the blood and other sterile body fluids to provide baseline data that can serve as an essential reference for monitoring resistance and empirical therapy changes. Thus, the present study investigated the cumulative incidence and antimicrobial susceptibility patterns from pathogens recovered from sterile fluids.

Material and Methods

Results

Discussion

In the present study, most bacterial species detected were gram-negative (when no S. epidermidis was included), with E. coli being the most frequent bacterial species detected in blood, CSF, and pleural fluid.

Regarding blood cultures, our results are similar to those reported in an Austrian study from 2006 to 2015 in which E. coli was the most common isolated pathogen (n = 2,869), followed by S. aureus (n = 1,439), Enterococcus spp. (n = 953), and Klebsiella spp. (n = 816) (Kreidl et al., 2019). Furthermore, a study in a seven-year North American study in which 24,179 cases of bloodstream infections were included, the most common organisms were coagulase-negative staphylococci (31% of isolates), followed by S. aureus (20%) and Enterococci (9%) (Wisplinghoff et al., 2004).

In our study, the most frequent species was E. coli (when no S. epidermidis was considered). It has been reported that this bacterial species is responsible for 48 per 100,000 person-years cases of bacteremia, increasing to 100 per 100,000 person-years in the 55–75 age group and over 300 per 100,000 person-years in the 75–85 age group (Bonten et al., 2021). These data underline the relevance of this bacterial species.

Commercial products dominate antimicrobial susceptibility testing methods in hospital laboratories, with relatively high accuracy. These methods have become better suited to fastidious species like S. pneumoniae, for which the need for red blood cells complicates the use of BMD. Compared with the BMD method, the proportion of penicillin-resistant S. pneumoniae was reported more frequently when routine, conventional methods were used. This was not observed for levofloxacin, erythromycin, trimethoprim-sulfamethoxazole, and vancomycin. A slight decrease in penicillin and cefotaxime resistance was observed in this study period compared to the previous decade, 2009–2018 (Garza-González et al., 2020), which might explain the continued use of pneumococcal conjugate vaccines since 2008. An increase in erythromycin resistance was observed, and a further increase is likely to be expected shortly, considering the use of azithromycin as an inflammatory aid in COVID-19 patients.

In blood cultures, the possibility of contamination must always be considered in interpreting positive results because microbes that are not in the bloodstream may be introduced into the bottle during blood collection (Gonsalves et al., 2009). Contamination is often due to organisms that can be part of the skin microbiota, such as S. epidermidis. In our study, the most frequent species detected was S. epidermidis, and according to our results, contamination seems excessive and points to the need for improving blood intake procedures. However, other pathogens detected in this study are not frequently observed in the skin (e.g., E. coli, K. pneumoniae. E. cloacae, S. marcescens, K. aerogenes, and P. mirabilis). Thus, they are most probably from the clinical specimen. A small sample volume is associated with difficulties in maintaining sterile conditions due to poor venous access (Gonsalves et al., 2009; Bekeris et al., 2005); thus, the contamination rate inversely correlates with blood volume (Gonsalves et al., 2009; Bekeris et al., 2005). Additionally, venipuncture, arterial access, or central venous access are associated with different contamination rates: 36%, 10%, and 7%, respectively (Gonsalves et al., 2009). Our study has no such data to verify these values, but laboratories followed the manufacturer’s recommendations regarding volume in general.

In this study, the drug resistance of pathogens from blood was similar to our previous reports (Garza-González et al., 2021; Garza-González et al., 2020; Garza-González et al., 2019). This study added data on drug susceptibility for Citrobacter freundii, Serratia marcescens, Proteus mirabilis, Morganella morganii, and Burkholderia cepacia, for which limited information is available in Mexico.

Regarding S. Typhi, the widespread use of fluoroquinolones has led to the emergence of decreased ciprofloxacin susceptibility. Our previous report, with only 10 clinical isolates included, showed 20% resistance (Garza-González et al., 2019). This work detected an 11% resistance (with 88 clinical isolates included).

Regarding the B. cepacia, trimethoprim-sulfamethoxazole remains a recommended first-line therapy (Avgeri et al., 2009). Our report detected 20.5% resistance for this drug; another first-line therapy, meropenem, showed a resistance of 5%. The primary alternative therapeutic agents beyond trimethoprim-sulfamethoxazole include ceftazidime and meropenem (Avgeri et al., 2009). This study showed that the high susceptibility to ceftazidime (0% resistance, at least in vitro) renders this antibiotic a good alternative in the studied populations.

The bacterial pathogens detected in CSF are various according to age. Between 16 and 50 years, Neisseria meningitidis and S. pneumoniae are frequently reported. In those over 50 years, Listeria monocytogenes and aerobic gram-negative bacilli are encountered (van deBeek et al., 2016). Furthermore, in immunocompromised individuals over 50 years of age, aerobic gram-negative bacilli and Salmonella spp. are frequently found (van deBeek et al., 2016). Other gram-negative bacteria and P. aeruginosa are pathogens found after neurosurgery or head trauma (Tunkel et al., 2017). Regardless of age, the most frequent causative agents isolated from CSF have been reported to be gram-negative bacteria, with A. baumannii, K. pneumoniae, and E. coli as the most frequently recovered species (Hu et al., 2019). In our study, similar results were observed, with E. coli being the most prevalent, if we omitted S. epidermidis.

S. epidermidis may have relevance in patients with hydrocephalus controlled by diverting or shunting the fluid around the obstruction and into a suitable body cavity. Shunts may be colonized primarily by skin organisms, with S. epidermidis being the most common cause of shunt colonization (Yakut et al., 2018; Bayston, 1989). In our population, S. epidermidis was the most frequent bacterial species detected. Whether this organism was associated with shunt infections needs further exploration.

In China, 244,843 strains from 44 teaching hospitals were analyzed in 2018 (14.8% from blood and 1.3% from CSF). In CSF only, 64.1% of K. pneumoniae and 60% of P. aeruginosa were resistant to carbapenem (29). Fortunately, we detected much lower percentages of resistance (4.9% and 31.3%). These data support the need to monitor drug resistance in specific populations.

Aerobic organisms are most implicated in pleural infection. When all populations are considered, streptococcal species are the primary cause at approximately 60%, followed by staphylococcal species and Enterococcus (Davies et al., 2010). The gram-negative aerobes cause about 15% and anaerobes nearly 14% of identified pathogens (Davies et al., 2010).

When causative agents are stratified, causative agents vary considerably by the site of acquisition, age, or comorbidities. For example, 50% of cases of community-acquired empyema are due to streptococci, and the remainder is due to staphylococci, anaerobes, and gram-negative bacilli (Maskell et al., 2005). However, in hospital-acquired empyema (associated with hospital-acquired pneumonia) or iatrogenic causes, staphylococci, gram-negative bacilli, Enterococcus species, and cefoxitin-resistant S. aureus are the most frequently implicated organisms. In pediatric patients, the most frequent isolate in pleural fluids reported is S. pneumoniae (up to 48%), followed by group A Streptococcus, S. aureus. In patients with comorbidities, especially diabetes or alcoholism, gram-negative bacteria are the most frequent (Maskell et al., 2005). In our study, E. coli and S. aureus were most frequently detected, with a significant role of P. aeruginosa as the causative agent. Unfortunately, we have no data on the comorbidities associated with these infections.

The selection of appropriate empiric therapy results in better outcomes in severe infections occurring in sterile fluids, i.e., blood, cerebrospinal and pleural fluids. The prevalent, most frequently isolated antibiotic-resistant pathogens in every hospital should guide the initial therapy selection. Also helpful is the knowledge of previous experiences of discordant therapy in bacteremia caused by frequent resistant pathogens like S. aureus or Enterobacteriaceae. Adjustments should be made according to the report on cultures and susceptibility (Kadri et al., 2018; Kadri et al., 2021). The results from this and other studies from the INVIFAR network will help in selecting the appropriate empiric therapy.

Part of the isolates was reported in a previous manuscript of the network, specifically, those collected from the second semester of 2019 and the second semester of 2020 (López-Jácome et al., 2021), exclusively from the centers that participated in both studies and from blood isolates.

In this study, each laboratory identified the strains and tested their susceptibilities using routine, conventional methods, including commercial microdilution systems. Each system has advantages and limitations, and the results vary widely by antimicrobial drugs, software versions, and cards used (Gajic et al., 2022).

Some studies have evaluated the performance of these instruments. For example, a multicenter evaluation showed that categorical agreement between the Phoenix system and the broth microdilution method for 2013 streptococcal isolates, including S. pneumoniae, ranged from 92% to 100% (Richter et al., 2007). Furthermore, the performance of the Phoenix, Vitek 2, and the MicroScan have been compared with the microdilution broth reference method for 311 clinical isolates of S. pneumoniae, and the overall essential agreement between each test was >95% (Mittman et al., 2009). Additionally, 109 S. maltophilia bloodstream isolates were analyzed, and very major errors were >.3% for trimethoprim-sulfamethoxazole (MicroScan, Phoenix), levofloxacin (MicroScan), and ceftazidime (all systems).

Limitations of this retrospective study are worth noting. First, we were unable to collect complete data on the age of the patients. Second, no clinical data were available to support the indication of the study or the relevance of the clinical isolate. Third, our results represent the combined data of general, mother and child, specialty hospitals, and other centers; thus, each hospital needs to address its results. Fourth, not all antibiotics were available from all centers; thus, some antibiotics are not included, such as levofloxacin for P. aeruginosa. Fifth, different methodologies were used for the detection of antibiotic susceptibility.

Conclusions

The results presented in this article represent the consolidated analysis of isolates from 45 centers. S. epidermidis was the most frequently recovered bacterial species from blood and CSF. Whether these isolates represent contamination or are associated with infection remains unclear. Gram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods can help detect resistance percentages for levofloxacin, cefotaxime, and vancomycin.