Pneumococcal Isolation from Adult Sputum Cultures During the COVID-19 and Post-Pandemic Period: A Retrospective Study

1. Introduction

Streptococcus pneumoniae has long been recognized as a leading cause of respiratory tract infections and invasive diseases, including pneumonia, bacteremia, and meningitis. Globally, the pathogen imposes a considerable burden, particularly among elderly individuals and patients with underlying comorbidities such as chronic pulmonary, cardiovascular, or renal diseases.[1] Prior to the COVID-19 pandemic, pneumococcal disease represented a significant public health concern; however, the epidemiological landscape was substantially influenced by the introduction of widespread non-pharmaceutical interventions such as social distancing, mask mandates, and lockdowns.[2,3]

International surveillance data reported a marked reduction in invasive pneumococcal disease during the early phase of the COVID-19 pandemic.[4,5] This phenomenon has been associated with decreased circulation of respiratory viruses, which are known to facilitate pneumococcal colonization and secondary bacterial infection. More recent reports suggest that pneumococcal activity may be gradually re-emerging following the relaxation of public health measures in certain regions.[6,7] These dynamic trends have generated renewed interest in the contemporary epidemiology of S. pneumoniae, particularly among adult populations with complex comorbidity profiles. However, whether this decline persists or is followed by a rebound in pneumococcal activity remains uncertain across different regions.

In Turkey, pneumococcal surveillance has primarily focused on pediatric populations and vaccine coverage studies.[8,9] Data describing pneumococcal isolation rates and antimicrobial susceptibility patterns in adult patients, especially within tertiary hospital settings, remain limited. Furthermore, the microbiological characteristics of pneumococcal isolates detected during the COVID-19 and post-pandemic period in Turkish adults have not been comprehensively described.

To address this gap, we conducted a retrospective laboratory-based surveillance study reviewing all adult sputum cultures processed at a tertiary training and research hospital between 1 October 2021 and 1 October 2023. The primary objective was to determine the frequency of S. pneumoniae isolation and to describe the clinical and antimicrobial susceptibility characteristics of detected isolates during the COVID-19 and post-pandemic period.

2. Materials and Methods

2.1. Ethical Approval and Informed Consent

The study protocol was reviewed and approved by the local Ethics Committee (Approval Number: 2023/65; Approval Date: October 12, 2023), in accordance with the Declaration of Helsinki and relevant national regulations. As this was a retrospective study using de-identified data, the requirement for informed consent was waived by the ethics committee.

2.2. Study Design and Setting

This retrospective, laboratory-based surveillance study was conducted at a tertiary care training and research hospital in Istanbul, Turkey. The study period extended from October 1, 2021, to October 1, 2023. All consecutive sputum cultures obtained from adult patients (≥18 years) as part of routine clinical care during this period were identified and systematically reviewed through the hospital’s microbiology database. No additional sampling or selective inclusion was performed. Relevant clinical data, including demographic characteristics, comorbidities, and admission details, were extracted from the hospital’s electronic medical records system.

2.3. Case Definition and Eligibility

Cases were defined as adult patients (≥18 years) with at least one sputum culture positive for S. pneumoniae during the study period. For the calculation of the pneumococcal isolation rate, all consecutive sputum cultures obtained from adult patients within the same period were included as the denominator. Repeated positive cultures from the same patient, if present, were considered a single case for descriptive analysis.

2.4. Data Collection

Data were extracted from the hospital’s electronic laboratory information system and electronic medical records. For all adult sputum cultures processed during the study period, the total number of samples was recorded to calculate the pneumococcal isolation rate. For patients with culture-confirmed S. pneumoniae, the following variables were collected: age, sex, smoking status (when available), major comorbidities (including diabetes mellitus, hypertension, cardiovascular or cerebrovascular disease, and chronic pulmonary conditions), indication for hospital admission, intensive care unit requirement, in-hospital outcome, specimen collection date, and antimicrobial susceptibility results, including minimum inhibitory concentrations (when available). These variables were selected to characterize the clinical context and microbiological features of confirmed cases.

2.5. Microbiological Procedures

Sputum samples were processed as part of routine clinical microbiology practice during the study period. Specimens were evaluated for quality using standard laboratory criteria prior to culture processing. Samples deemed acceptable were inoculated onto appropriate culture media, including sheep blood agar, and incubated under conventional conditions. Bacterial identification was performed using the automated identification system routinely employed in the laboratory at the time of analysis. When required, confirmatory phenotypic methods such as assessment of alpha-hemolysis and optochin susceptibility testing were applied in accordance with standard laboratory procedures.

2.6. Antimicrobial Susceptibility Testing

Antimicrobial susceptibility testing was performed as part of routine laboratory practice using the automated system employed during the study period. Results were interpreted according to the breakpoint criteria defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines applicable at the time of testing. Susceptibility categories were reported as susceptible (including susceptible, increased exposure) or resistant. Minimum inhibitory concentrations (MICs) were recorded when available in the laboratory information system.

2.7. Outcomes

The primary outcome was the pneumococcal isolation rate, defined as the proportion of S. pneumoniae-positive sputum cultures among all adult sputum samples processed during the study period. In addition, the antimicrobial susceptibility profiles of confirmed isolates were evaluated. Secondary outcomes included the clinical characteristics of patients with culture-confirmed S. pneumoniae, including comorbidity burden, intensive care unit requirement, in-hospital outcome, and the temporal distribution of detected isolates across the study period.

2.8. Statistical Analysis

The pneumococcal isolation rate was calculated as the proportion of S. pneumoniae-positive cultures among all adult sputum samples processed during the study period. Exact binomial 95% confidence intervals (CIs) were calculated for the isolation rate. Given the limited number of positive isolates, all other analyses were descriptive. No formal comparative statistical analyses were performed.

3. Results

During the study period (October 1, 2021–October 1, 2023), a total of 3,433 adult sputum cultures were processed at the tertiary care center. S. pneumoniae was isolated in three cases, corresponding to a pneumococcal isolation rate of 0.087% (95% CI: 0.018%–0.255%). No additional pneumococcal isolates were identified from other respiratory or sterile site cultures during the same period.

All positive cases occurred in male patients aged 45 to 81 years (median: 57 years). Two patients were ex-smokers with significant smoking histories (30 and 50 pack-years, respectively), while one had never smoked. Each patient had at least one underlying comorbidity, including cardiovascular disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus, or hyperthyroidism. In all three cases, pneumonia developed during hospitalization for non-infectious primary conditions (vascular access revision, cerebrovascular event, and orthopedic trauma), which prompted microbiological investigation. The demographic and clinical characteristics of patients with culture-confirmed S. pneumoniae are summarized in Table 1.

Antimicrobial susceptibility testing results are summarized in Table 2.

All isolates were susceptible to fluoroquinolones (levofloxacin and moxifloxacin), rifampicin, tetracycline, chloramphenicol, and ceftriaxone. One isolate (Patient 1) demonstrated resistance to erythromycin (MIC ≥8 µg/mL) and clindamycin (MIC ≥1 µg/mL). Trimethoprim/sulfamethoxazole showed intermediate susceptibility across all three isolates. None of the isolates met criteria for multidrug resistance.

The detected cases were distributed sporadically over the study period without evidence of temporal clustering. All patients responded clinically to targeted antimicrobial therapy, and no in-hospital mortality was observed.

4. Conclusions

This retrospective laboratory-based surveillance study demonstrates an extremely low pneumococcal isolation rate from adult sputum cultures in a tertiary care center over a two-year period encompassing the COVID-19 and post-pandemic era. Among 3,433 sputum cultures processed, only three yielded pneumococcal growth, corresponding to an isolation rate of 0.087% (95% CI: 0.018%–0.255%). Although sputum cultures were frequently processed during the study period, culture-confirmed detection of S. pneumoniae was rare. All identified cases occurred in male patients with underlying comorbidities, and pneumonia developed during hospitalization for non-infectious primary conditions. Given the limited number of isolates, these observations should be interpreted cautiously.

The low culture yield observed in our cohort is consistent with recent epidemiological shifts reported globally in the wake of the COVID-19 pandemic. Non-pharmaceutical interventions (e.g., masking, physical distancing), reduced transmission of respiratory pathogens, and changes in healthcare-seeking behavior have collectively led to a decline in community-acquired pneumococcal disease.[10]

Furthermore, empirical use of antibiotics—especially macrolides and beta-lactams—in outpatient and inpatient settings may have reduced culture positivity, either by suppressing viable pneumococci or altering the airway microbiome.[11]

Another plausible contributor is the impact of adult pneumococcal vaccination programs. Turkey introduced pneumococcal conjugate vaccines into the national childhood immunization schedule in 2008 with PCV7, which was replaced by PCV13 in 2011 as part of the routine program.[8] Recent studies have also shown that targeted adult vaccination, particularly among the elderly and high-risk groups, can significantly reduce invasive pneumococcal disease and possibly carriage. Targeted adult immunization, particularly in high-risk groups such as the elderly and those with chronic diseases, may further reduce pneumococcal disease burden in hospitalized populations.[13]

Microbiologically, all isolates in our cohort were susceptible to ceftriaxone, moxifloxacin, levofloxacin, rifampicin, and tetracycline, agents commonly employed in empirical pneumonia treatment. These findings are in line with recent surveillance studies from Turkey and Europe, which report high susceptibility rates to beta-lactams and fluoroquinolones in respiratory S. pneumoniae isolates.[14]

However, resistance to macrolides and lincosamides was observed in one patient, with erythromycin MIC ≥8 µg/mL and clindamycin resistance. This pattern reflects trends showing rising macrolide resistance, particularly in regions with extensive outpatient macrolide use.[14,15]

The detected intermediate susceptibility to trimethoprim/sulfamethoxazole (TMP-SMX) in all isolates is also noteworthy. Previous studies have reported substantial variability in TMP-SMX resistance among Streptococcus pneumoniae isolates, with approximately one-third of isolates showing resistance in some settings, highlighting the heterogeneity in susceptibility patterns.[16] Although not a first-line agent for pneumococcal pneumonia, TMP-SMX susceptibility data may still provide supportive information for step-down or oral therapy decisions in selected cases, particularly in resource-limited settings.

Importantly, none of the isolates in our study met criteria for multidrug resistance (MDR), a reassuring finding given the recognized presence of MDR pneumococcal lineages reported in surveillance studies.[17] However, the small sample size precludes broader conclusions, and continuous surveillance is essential to monitor emerging resistance patterns.

The present findings also highlight the diagnostic limitations of sputum cultures. Pre-analytical factors such as prior antibiotic exposure, poor sputum quality, or delayed transport can reduce yield.[11] Additionally, in the elderly or debilitated population, lower respiratory tract infection may present atypically, further complicating microbiological confirmation.[18] Nonetheless, the detection of S. pneumoniae in these patients—each with documented clinical deterioration and radiographic findings—supports its role as a relevant pathogen in selected hospital-acquired or secondary pneumonia cases.

5. Limitations

This study has several important limitations. First, the retrospective design limits the ability to establish causal relationships and prevents direct comparison with the pre-pandemic period. Second, the extremely small number of pneumococcal isolates restricts generalizability and limits the scope of statistical inference beyond descriptive analysis. Third, only sputum cultures were evaluated; data from other respiratory or sterile site specimens were not systematically included, which may have led to underestimation of the true pneumococcal disease burden. In addition, information on vaccination status, prior antibiotic exposure, and radiological findings was not uniformly available and therefore could not be systematically analyzed. Finally, variability in sputum specimen quality and other pre-analytical factors may have influenced culture yield.

6. Conclusions

This retrospective laboratory-based surveillance study demonstrates an extremely low pneumococcal isolation rate from adult sputum cultures in a tertiary hospital during the COVID-19 and post-pandemic period. Although direct comparison with pre-pandemic data was not possible, the observed findings are consistent with international reports describing reduced pneumococcal detection during the pandemic era. The limited number of isolates prevents definitive conclusions regarding resistance trends; however, susceptibility to commonly used antimicrobial agents was largely preserved. Continued microbiological surveillance remains essential to monitor evolving epidemiological patterns and antimicrobial susceptibility profiles.

Ethics Approval: The study protocol was reviewed and approved by the Ethics Committee of Fatih Sultan Mehmet Training and Research Hospital (Approval Number: 2023/65; Approval Date: October 12, 2023), in accordance with the Declaration of Helsinki and relevant national regulations. As this was a retrospective study using de-identified data, the requirement for informed consent was waived by the ethics committee.