Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical, and microbiological characteristics, 2016-2018.

PURPOSE: No data are available on severe community-acquired pneumonia (CAP) in the French overseas department of Reunion Island. This is unfortunate as the microorganisms responsible for the disease are likely to differ from those in temperate regions due to a tropical climate and proximity to other islands of the Indian Ocean region. The aim of this study was to assess the epidemiological, clinical, prognosis, and microbiological characteristics of patients with severe CAP in Reunion Island.
MATERIALS AND METHODS: This retrospective study evaluated all patients with CAP aged >18 years and hospitalized in one of the two intensive care units of Reunion Island between 2016 and 2018. Microorganisms were identified by culture from blood and respiratory samples, multiplex polymerase chain reaction from respiratory samples, urinary antigen tests, and serology.
RESULTS: Over the study period, 573 cases of severe CAP were recorded, with a mean incidence of 22 per 100,000 person-years. The most frequently isolated microorganism was influenza (21.9%) followed by Streptococcus pneumoniae (12%). The influenza virus was detected in affected patients all year round. Twenty-four patients with severe CAP came from another island of the Indian Ocean region (4.2%), mainly Madagascar (>50%). Two of these patients presented with melioidosis and 4 were infected with Acinetobacter spp.
CONCLUSIONS: Our findings have major implications for the management of severe CAP in tropical regions. The most frequently isolated microorganism in patients with severe CAP in Reunion Island is influenza followed by S. pneumoniae. Physicians should be aware that influenza is the main cause of severe CAP in patients living in or returning from Reunion Island, where this virus circulates all year round.

Introduction

Community-acquired pneumonia (CAP) is an acute infection of the lung parenchyma that is acquired outside hospital or health care facilities. It is the most common life-threatening infectious disease. National and international guidelines for the management of severe CAP [1, 2] are based on data collected in regions with a temperate climate, where Streptococcus pneumoniae, viruses, and Legionella are the main cause of the disease [3, 4]. Accordingly, they recommend to initiate antibiotic therapy effective against all strains of S. pneumoniae and Legionella (i.e., combination therapy with cephalosporin and a macrolide or monotherapy with respiratory fluoroquinolone) [5] and to consider the possibility of influenza infection during the winter season [6].

These guidelines are also applied in tropical regions, where the microorganisms responsible for the disease are likely to differ from those in temperate regions. This is the case in Reunion Island, a French overseas department with a population of 850,000 inhabitants located in the Indian Ocean region. This tropical island is characterized by two distinct seasons, the hot and humid southern summer from December to May and the milder and drier southern winter the rest of the year. Patients from the entire Indian Ocean region (Madagascar, Mauritius, and the Comoros Archipelago) are regularly evacuated to Reunion, both for reasons of proximity and because the medical infrastructure meets European standards (P3 microbiology laboratories, coronarography, all types of surgeries, circulatory assistance, etc.). This raises the possibility that microorganisms endemic to Madagascar and other neighboring islands, such as Burkholderia pseudomallei [7] and Yersinia pestis [8], are responsible for some of the cases of severe CAP observed on the island. In spite of this, no comprehensive study of the etiology of severe CAP in Reunion have been conducted to date. A better knowledge of the microbiological characteristics of severe CAP in the region could improve the management of residents or travelers from Reunion Island by helping physicians choose the best antimicrobial treatment according to the season.

The aim of this study was to assess the epidemiological, clinical, prognosis, and microbiological characteristics of patients with severe CAP hospitalized in intensive care unit (ICU) in Reunion Island.

Materials and methods

Selection of the study sample

We performed a retrospective chart review of all adult patients diagnosed with severe CAP and hospitalized in one of the two ICUs of Reunion Island (Félix Guyon University Hospital and Saint Pierre University Hospital) between January 2016 and December 2018.

Ethics

A written notice was provided to all participants or their legally authorized representative. Informed consent was not needed due to the retrospective and non-interventional nature of the study.

This observational study was approved by the French Ethics Committee of Infectious Disease and Tropical Medicine (CER-MIT) and declared to the French National Commission for Data Protection and Liberties (CNIL, #2206739). It complies with the Strengthening the Reporting of Observational studies in Epidemiology recommendations statement [9].

Definitions

Community-acquired pneumonia was defined as pneumonia acquired outside hospital and diagnosed within 48 hours of hospital admission. Diagnosis was established in the presence of a new lung infiltrate on chest x-ray or computed tomography scan together with one or more of the following symptoms and signs: fever >38°C, cough, expectoration, chest pain, dyspnea, and signs of invasion of the alveolar space [10].

A severe case of CAP was defined as any patient hospitalized in ICU with 1 of the major criteria and/or 3 or more of the minor criteria established by the American Thoracic Society [1]. Major criteria were septic shock with need for vasopressors and respiratory failure requiring mechanical ventilation. Minor criteria were respiratory rate >30 breaths/min, PaO2/FIO2 ratio <250, multilobar infiltrates, confusion or disorientation, blood urea nitrogen level >20 mg/dL, white blood cell count <4 G/L, platelet count <100 G/L, hypothermia <36°C, and hypotension requiring aggressive fluid resuscitation.

Microbiological investigations

Blood and respiratory samples (sputum samples from non-intubated patients and tracheal or bronchoalveolar lavage from intubated patients) were collected from all patients. Microorganism identification was performed on both types of samples using Gram staining followed by culturing for definite identification. Alternatively, identification was performed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Respiratory samples were tested by multiplex polymerase chain reaction (PCR) (Seegene Allplex™ respiratory panel, Eurobio-ingen, Les Ulis, France) for the following microorganisms: influenza, respiratory syncytial virus, adenovirus, enterovirus, parainfluenza, human metapneumovirus, human bocavirus, rhinovirus, coronavirus (NL63, 229E, and OC43), Chlamydia pneumoniae, Mycoplasma pneumoniae, Legionella spp, Haemophilus influenzae, S. pneumoniae, Bordetella pertussis, and B. parapertussis.

Pneumococcal and Legionella urinary antigen tests were routinely performed on admission to ICU.

Serology for atypical respiratory microorganisms was performed at the physician’s discretion.

Data collection

Patient comorbidities were recorded at hospital admission.

Clinical and biological data were collected at the time of CAP diagnosis.

Average rainfall data for the 2016–2018 period were obtained from Météo France, Bureau of Meteorology, Saint-Denis, Reunion Island.

Study outcome

The primary outcome was to determine the ICU mortality and morbidity of patients with CAP.

The secondary outcome was to identify the microorganisms responsible for CAP in patients hospitalized in ICU.

Statistical analysis

Results were expressed as total number (percentage) for categorical variables and as median [25th-75th percentiles] for continuous variables. Continuous variables were compared using the Mann-Whitney test and categorical variables using the Chi-square test or Fisher’s exact test, as appropriate. Survival functions in ICU at 30 days were estimated using the Kaplan-Meier method and compared using the log-rank test. A P value <0.05 was considered significant. Analyses were performed using the SAS statistical software (8.2, Cary, NC, USA).

Results

Incidence and isolated microorganisms

From January 2016 to December 2018, 1,283 patients were admitted to ICU for suspected or confirmed lower tract respiratory infection. Of these, 710 patients were excluded (12 were <18 years old, 698 had nosocomial pneumonia or non-infectious pneumonia). The remaining 572 patients formed the study cohort. The mean incidence of severe CAP was 22 per 100,000 person-years. The median age was 62 [52-73] years and the median simplified acute physiology score II on admission was 44 [31-57]. Patients presented with acute respiratory distress syndrome in 396 cases (69.2%) and with sepsis or septic shock in 347 cases (60.7%). Patient characteristics at ICU admission are shown in Tables 1 and 2.

Table 1

Clinical characteristics at intensive care unit admission.

Clinical characteristics	Missing data	Total	Influenza CAP	Non-Influenza CAP	P-value
		(n = 572)	(n = 125)	(n = 447)
Age (years)	0	62 [52–73]	61 [48.3–69]	63 [52.2–74]	0.099
Male	0	376 (65.7)	73 (58.4)	303 (67.8)	0.013
Body mass index (kg/m2)	45	24.1 [21.4–29]	25.47 [22–29.9]	23.8 [21.1–28.63]	0.079
1Foreign residence	0	26 (4.5)	3 (2.4)	23 (5.1)	0.091
Duration of symptoms before ICU admission (days)	0	2 [1–5]	3 [2–6]	2 [1–5]	0.018
2CURB-65 score	8	3 [2–3]	3 [2–4]	3 [2–3]	0.122
SAPS II	12	53 [28–68]	55 [37–58.5]	48.5 [28.7–68.7]	0.795
Pulmonary abscess	0	38 (6.6)	7 (5.6)	31 (6.9)	0.147
Influenza-like illness	0	175 (30.6)	68 (54.4)	107 (23.9)	<0.001
Immunosuppression	0	47 (8.2)	9 (7.2)	38 (8.5)	0.136
Corticosteroids	0	53 (9.3)	7 (5.6)	46 (10.3)	0.04
3Hazardous alcohol use	3	159 (27.8)	26 (20.8)	133 (29.8)	0.13
Chronic obstructive pulmonary disease	0	144 (25.2)	26 (20.8)	118 (26.4)	0.042
Asthma	0	33 (5.8)	13 (10.4)	20 (4.5)	0.009
Hypertension	0	248 (43.3)	56 (44.8)	192 (43)	0.076
Chronic renal failure with dialysis	0	28 (4.9)	5 (4)	23 (5.1)	0.171
Diabetes mellitus	0	197 (34.4)	48 (38.4)	149 (33.3)	0.048
Liver cirrhosis	0	22 (3.8)	4 (3.2)	18 (4.0)	0.2
Cancer < 4 months	0	51 (8.9)	6 (4.8)	45 (10.1)	0.026
History of congestive heart failure	0	114 (19.9)	18 (14.4)	96 (21.5)	0.022
Pregnancy	0	7 (1.2)	2 (1.6)	5 (1.1)	0.294

Results are expressed as n (%) or median [25th-75th percentiles], as appropriate.

CAP: Community-acquired pneumonia; ICU: Intensive care unit; SAPS 2: Simplified acute physiology score 2 [11].

1Wounded and sick patients transported from foreign countries.

2CURB-65 (confusion: 1 point; blood urea nitrogen>19mg per dl:1 point; respiratory rate>30:1 point; systolic blood pressure<90mmHg and/or diastolic blood pressure<60mmHg:1 point; age>65 years:1 point) [12].

3Alcohol Use Disorders Identification Test Consumption ≥ 4 for men or 3 for women [13].

Table 2

Prognostic factors and laboratory findings at intensive care unit admission.

Variables	Missing	Total	Influenza CAP	Non-Influenza CAP	P-value
	data	(n = 572)	(n = 125)	(n = 447)
Prognostic factors
Temperature (°C)	23	38 [36.6–38.7]	38.3 [37.1–39]	37.7 [36.5–38.6]	0.017
Glasgow Coma Scale score	1	15 [3–15]	15 [3–15]	15 [3–15]	0.348
Extracorporeal membrane oxygenation	0	21 (3.7)	10 (8)	11 (2.5)	0.005
Mechanical ventilation	0	325 (56.8)	76 (60.8)	249 (55.7)	0.049
Non-invasive ventilation	0	122 (21.3)	31 (24.8)	91 (20.4)	0.054
High-flow oxygen therapy	0	72 (12.6)	17 (13.6)	55 (12.3)	0.11
Renal replacement therapy	0	74 (12.9)	19 (15.2)	55 (12.3)	0.08
Catecholamines	0	283 (49.5)	64 (51.2)	219 (49)	0.073
Pa02/FiO2 ratio (mmHg)	6	166 [110.25–240]	152 [97.5–205.5]	179.5 [115–252.8]	0.003
Laboratory findings
Creatinine level (μmol/L)	0	109 [70–178]	106 [70–148.25]	110 [71.25–187]	0.335
Total bilirubin level (μmol/L)	12	10 [6–16]	9 [6–15]	11 [6–16]	0.414
Prothrombin time (%)	8	70 [55–83]	72.5 [58.75–87]	67 [53–81]	0.029
Platelet count (G/L)	1	188 [129–271]	158 [119–218]	203.5 [136–285.5]	<0.001
Leucocyte count (G/L)	0	11.7 [7.5–16.3]	8.9 [5.5–14.5]	12.1 [8.15–16.65]	<0.001
Lactate level (mmol/L)	9	1.95 [1.3–3.4]	2 [1.3–3.2]	1.9 [1.3–3.5]	0.859
Creatine phosphokinase (mg/dL)	18	210 [87–604]	260 [122–947]	184 [83–513]	0.036
Hemoglobin level (g/dL)	0	12 [10.1–13.6]	12.75 [11.25–14]	11.76 [10–13,5]	0.001
Alanine aminotransferase level (UI/L)	11	28 [17–51.25]	32 [16–55]	26 [17–51]	0.271
Troponin level (ng/dL)	24	37 [16–104]	25 [11–82]	38 [18–116.25]	0.017
C-reactive protein level (mg/L)	54	170 [73.25–304.25]	148 [71.5–250.5]	177.5 [73.1–324]	0.558

Results are expressed as n (%) or median [25th-75th percentiles], as appropriate.

The microorganism(s) responsible for severe CAP were identified in 67% of cases. The most frequently isolated microorganisms were influenza (21.9%), S. pneumoniae (12%), Staphylococcus spp (10.8%), Enterobacteriaceae (9.8%), and H. influenzae (7.5%). Panton-Valentine leukocidin-positive Staphylococcus aureus accounted for 11.3% of all Staphylococcus spp strains. Legionella pneumophila and other intracellular bacteria were responsible for 3% of cases (Table 3). Other isolated viruses were rhinovirus in 10 cases (1.7%), human metapneumovirus in 9 cases (1.6%), coronavirus OC43 in 9 cases (1.6%), parainfluenza in 9 cases (1.6%), respiratory syncytial virus in 8 cases (1.4%), and adenovirus in 2 cases (0.3%). In the group of patients with influenza CAP, infection was polymicrobial in 52 cases (41.6%).

Table 3

Isolated microorganisms.

Microorganisms	Total	Influenza CAP	Non-Influenza CAP
	(n = 572)	(n = 125)	(n = 447)
Viruses	168 (29.3)	125 (100)	43 (9.6)
Bacteria	283 (49.5)	50 (40)	233(52.1)
Staphylococcus spp	62 (10.8)	24 (19.2)	38 (8.5)
Panton-Valentine Leukocidin-positive	7 (1.2)	4 (3.2)	3 (0.7)
Streptococcus pneumoniae	69 (12)	16 (12.8)	53 (11.8)
Haemophilus influenzae	43 (7.5)	5 (4)	38 (8.5)
Enterobacteriaceae	56 (9.8)	3 (2.4)	53 (11.8)
Non-fermenting gram-negative bacilli	26 (4.5)	2 (1.6)	24 (5.4)
Legionella	9 (1.5)	0	9 (2)
Intracellular	9 (1.5)	0	9 (2)
Fungi	8 (1.4)	2 (1.6)	6 (1.3)

Results are expressed as n (%).

Polymicrobial infection was found in 52 cases of influenza CAP (41.6%).

Bacteremia was found in 97 cases of severe CAP (16.9%).

Bacteremia was found in 44 cases of influenza CAP (35.2%) and in 53 cases of non-influenza CAP (11.8%).

The incidence of influenza vs. S. pneumoniae according to rainfall is shown in Fig 1.

Fig 1

Incidence of influenza vs. S. pneumoniae according to rainfall, 2016 to 2018, Reunion Island.

Twenty-four patients with severe CAP came from another island of the Indian Ocean region (4.2%), mainly Madagascar (>50%). Two of these patients presented with melioidosis (which is caused by B. pseudomallei) and 4 were infected with Acinetobacter spp (2 with Acinetobacter baumannii and 2 with A. pittii).

Prognosis

Over the study period, ICU mortality for the entire cohort was 20.8%. Survival rates according to microorganism are shown in Fig 2.

Fig 2

Survival rate according to microorganism using Kaplan–Meier analysis.

In univariate analysis, mortality was higher in patients with influenza CAP (24%) than in patients with non-influenza CAP (18.9%, P = 0.04).

The median duration of ICU stay was 7 [4-17] days in patients with influenza CAP vs. 6 [3-11] days in patients with non-influenza CAP (P = 0.018).

The median duration of mechanical ventilation was 4 [0-14] days in patients with influenza CAP vs. 2 [0-8] days in patients with non-influenza CAP (P = 0.04).

The need for extracorporeal membrane oxygenation was 8% in patients with influenza CAP vs. 2.5% in patients with non-influenza CAP (P = 0.005).

Discussion

This is the first epidemiological study to assess the clinical, microbiological, and prognostic characteristics of severe CAP in Reunion Island. It is also one of the rare studies on CAP in the Indian Ocean region [14, 15]. The incidence of severe CAP in our cohort was 22 per 100,000 person-years. The most frequently isolated microorganism was influenza (21.9%) followed by S. pneumoniae (12%). These epidemiological data can help to implement appropriate anti-infective treatment in residents or travelers from Reunion Island with severe CAP [16].

The rate of microbiological identification in our study was relatively high (68.3%) compared to other studies on the subject (around 50%) [3, 17–20]. This difference may be explained by our use of multiplex PCR, which allowed to detect both viral and bacterial agents of the disease. As in our study, recent studies using PCR for microbiological identification [20-22] found viruses (and especially influenza) to be the most common cause of severe CAP. Thus, in the 2016 retrospective study conducted by Visseaux et al. in mainland France [21], 29.2% of 5,000 ICU patients with severe CAP had a viral infection. This finding is in line with our study, which detected viruses in 29.3% of patients with severe CAP. By contrast, the influenza virus accounted for 74.7% of all detected viruses in our study compared to 34.4% in the study by Visseaux et al. Siow et al. [23] have stressed the importance of using PCR for the detection of viruses causing severe CAP in tropical environments, where the incidence of viral infections is less dependent on the seasons than in temperate regions [24, 25]. In our study, this approach showed that influenza circulates all year round in Reunion Island. In spite of this, peaks of influenza incidence were observed during the southern winter and monthly incidence was found to be inversely proportional to temperature and rainfall. Several other studies conducted in tropical regions have found an association between seasons and the occurrence of influenza infections [25-29]. However, the physio-pathological explanation for this association remains to be established [24].

In our cohort, S. pneumoniae was the second (12%) most frequently isolated microorganism. This contrasts with most available studies, which identify S. pneumoniae as the main cause of severe CAP. However, many of these studies do not provide the incidence of viral infections [1, 2, 5, 18, 23] or underestimate it due to the non-systematic use of PCR for microorganism detection. In the last epidemiological study on severe CAP in Reunion Island, Paganin et al. [18] identified S. pneumoniae (42.9%) and Klebsiella pneumoniae (22.4%) as the main cause of the disease. Yet, this 2004 study did not establish the viral etiology of severe CAP because multiplex PCR was not systematically used in local ICUs at the time.

In our study, 2 patients returning from Madagascar presented with melioidosis. Given the recent emergence of B. pseudomallei in the Indian Ocean islands [7], clinicians and microbiologists should consider melioidosis as a differential diagnosis in patients returning from the region, in particular from Madagascar. Other atypical microorganisms were detected, namely 2 strains of A. baumannii and 2 strains of A. pittii, with a mortality of 50%. While Acinetobacter spp strains are mainly known as nosocomial infectious agents, they have been shown to cause severe CAP in tropical areas. Thus, an observational study [30] conducted in Australia reported 41 cases of CAP caused by Acinetobacter spp, with A. baumannii accounting for 85% of strains. In that study, 88% of infectious episodes occurred during the rainy season, and 80% of patients required hospitalization in ICU.

The mortality rate for our entire cohort was 20.8%. This figure is consistent with those reported in the recent studies by Ferrer et al. (22%) [31] and Cavallazzi et al. (27%) [32]. By contrast, a UK study found mortality to reach 50% in patients with CAP hospitalized in ICU [33]. In the study conducted by Dupuis et al. in mainland France, hospital mortality was 22.8% in a cohort of 1,665 patients with severe pneumococcal CAP [34]. In our study, mortality and morbidity (including the need for extracorporeal membrane oxygenation and mechanical ventilation) were higher in patients with influenza CAP than in those with non-influenza CAP. Likewise, in the Spanish study by Abelleira et al., patients with CAP caused by influenza A H1N1 had a poorer prognosis than those with non-influenza CAP [35]. In a study conducted during the 2009 AH1N1 pandemic, Vandroux et al. [36] found mortality and the need for extracorporeal membrane oxygenation to be extremely high in Reunionese patients with AH1N1 influenza. Interestingly, Vandroux et al. reported numerous co-infections (31%), nearly half of which were caused by influenza and S. aureus. This is consistent with our results, since 41.6% of influenza infections were polymicrobial in our cohort, with half of them involving S. aureus. Other studies have found that mixed viral-bacterial infections are associated with an increased risk of mortality in patients with severe CAP [37, 38].

In line with the recommendations of the Infectious Diseases Society of America and the World Health Organization, the French Society of Infectious Disease and the French National Authority for Health recommend initiating curative treatment with oseltamivir in patients at risk of severe influenza [39]. Several recent studies confirm the potential benefit of early treatment with oseltamivir [40-43].

Our study has many limitations. First, the retrospective nature of the study could have introduced biases in our results. Second, only patients with severe CAP were included in the sample, which means that our results do not reflect the exact etiological agents of CAP in Reunion Island. Third, since our study covers the 2016–2018 period, it does not account for changes in the ecology of severe CAP that likely resulted from the COVID-19 pandemic and the implementation of social distancing measures [44-46]. Lastly, in the absence of multivariate analysis, we cannot discard the possibility that the difference in mortality rates observed between patients with influenza CAP vs. non-influenza CAP is due to the fact that the first group of patients had more comorbidities (age over 65 years, asthma, diabetes mellitus, etc.).

Conclusion

Our findings have major implications for the management of severe CAP in tropical regions. The most frequently isolated microorganism in patients with severe CAP in Reunion Island is influenza followed by S. pneumoniae. Physicians should be aware that influenza is the main cause of severe CAP in patients living in or returning from Reunion Island, where this virus circulates all year round.

(XLS)

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23 Jul 2021

PONE-D-21-05049

Severe community-acquired pneumonia in Reunion Island:Epidemiological, clinical and microbiological characteristics, 2016-2018

PLOS ONE

Dear Dr. Allou,

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While your paper addresses an interesting question, both reviewers expressed significant concern both about the presentation as well as the readability of the manuscript and did not recommend publication in its present form. In particular, both reviewers voice a number of concerns regarding the used methodology for data collection and analysis, and these comments need to be addressed carefully.  Please see reviewers’ insightful comments below. In addition, the quality of the language needs to be improved, please have a fluent, preferably native, English-language speaker thoroughly copyedit your manuscript for language usage, spelling, and grammar.

Personally, I found the following points need to be clarified:  1. Prevalent pathogens for CAP are influenza, S. penumoniae. How does this compare to nosocomial pneumonia? 2. CAP caused by influenza and S. penumoniae is year round, however, the authors indicated the rainfall play a role in the case of CAP.  From the figure, it appears more case for influenza CAP in dry season. Any studies on influenza CAP related to the same phenomenon? 3. The mortality rate is higher for influenza CAP, is this same from other region?

Specific comments:

Line 54, 97 “All consecutive patients…” I am not sure consecutive is the right adj. to use.  Suggest changing to “All patients…”

Line 79 – 81, is there any CAP data in nearby area, Madagascar for example?

Line 79, 81 &118, change “legionella” to “Legionella” since genus used alone should be capitalized and italicized.

Line 82,153, 194, 233 & 301,Streptococcus pneumonia should be “S. pneumoniae”

Line 116 – 117, change “Chlamydia pneumonia, Mycoplasma pneumonia, Legionella spp, Haemophilus influenza, Streptococcus pneumoniae and Bordetella (para) pertussis.” to “Chlamydia pneumoniae, Mycoplasma pneumoniae, Legionella spp, Haemophilus influenzae, S. pneumoniae, Bordetella pertussis, and B. prarpertussis.”

Line 142, please rephrase “…(incidence of 22 per 100,000 person- years)” for clarity.  Did the author mean 22 per 100,000 person per year?

Line 154, Staphylococcus should be italicized.

Line 155, “Haemophilus influenza” should be “H. influenzae”

Line 155 – 156, “Legionella pneumophila” should be “L. pneumophila”

Table 3, “Haemophilus influenza” should be “Haemophilus influenzae”

Line 193 – 195, it is not clear about the correlation between rainfall and CAP, please expand the explanation.

Line 200 – 206, maybe I missed something, I am not clear on the relevance of the risk factors for influenza with CAP?  How about risk factor associated with S. pneumoniae or CAP in general?

Line 220 – 222, please clarify the relevance of this statement.

Line 248, change “K. pneumoniae” to “Klebsiella pneumonia” since this is the first time Klebsiella was mentioned.

Line 274, Actinobacter should be italicized.

Line 285, “Staphylococcus aureus” should be “S. aureus”

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Reviewer #1: Yes

Reviewer #2: No

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: No

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Editor PLOS ONE,

Thank you for sending me this manuscript for review. The investigators studied clinical and microbiological characteristics of patients with severe pneumonia who were admitted to the ICUs. The manuscript is of interest, however, several points need to be highlighted and revised as follow.

Abstract

Editing error: “causatives”

Conclusions are not based on the results. Also, the recommendation of cephalosporin and oseltamivir needs revision to reflect the study findings and may lead to increased antimicrobial resistance.

Introduction

Some general statements require evidence and to be specific, for example:

Initiate antibiotic therapy against all strains of S pneumonia and Legionella. This is a general statement that needs to be more specific on the empiric use of antimicrobials.

Methods

The study was conducted on ICU admitted patients, and they may not represent the study objectives rather than only severe cases that required ICU admission. So, study objectives need to be changed accordingly.

It’s not clear too, how data were collected, was it a retrospective chart review?

Statistical analysis

Line 5: First time mentioned abbreviation, the full name should be provided.

Also, the statement is not clear: “Risk factors of influenza PAC in bivariate analysis with P<0.1 were entered into a multivariate logistic regression analysis using backward selection with P <0.05”.

The reported incidence in the results section was different from the abstract and discussion, should be revised.

Table (1), abscess was mentioned, what does it refer to what type of abscess and which site?

Table (1), duration between symptoms and ICU admission, was it days?

Table (1), what does it mean of reporting the p-value as zero? (for influenza-like illness)

Table (1), how hazardous alcohol use was assessed, what definition was used, and how data were collected?

Table (1), what does footnote 2 refer to?

Did the investigators collect any vaccination histories on influenza or pneumococcal vaccines among the study participants?

Table (3), footnote … “…. during flu cases” need revision.

What is “flu syndrome” mentioned in line 201?

Higher leukocyte counts mentioned in line 204 is not a risk for severe influenza as per the odds ratio presented.

Line 212 need revision

Discussion

The second highest cause of mortality and years of life lost. Was there a difference between mortality and years of life lost?

in-ICU mortality in this study was lower than previously reported. Any specific reasons or contributing factors to be discussed?

Editing, line 253, “….. we find” should “found”

What about the impact of empirical use of antimicrobials on the detection of organisms that have been reported in other reports.

The investigators included a paragraph in the discussion about climate change and influenza types, although they didn’t provide a specific discussion or explored the relevance to the study.

Conclusions should be revised to reflect the study findings.

Also, the recommendation of probabilistic antimicrobials and oseltamivir to every patient should be revised taking into consideration the potential risk for antimicrobial resistance and definition of severe pneumonia that may not be specific to be applicable in several care settings.

Figure (2), worst survival was observed for cases with S pneumonia, this needs further discussion

Figure (1) (which is also written as figure (2)), about rainfall and influenza, showed three peaks of rainfall but not clear of an association with the occurrence of influenza or pneumococcal infection, more elaboration in this regard is required.

Reviewer #2: Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical and microbiological characteristics, 2016-2018 (Manuscript No. PONE-D-21-05049)

In their manuscript, de Mangou et al. present valuable data derived from a retrospective cohort of patients admitted and diagnosed with severe CAP at Reunion Island between 2016 and 2018. However, significant scarcities of methodology detailed below could be identified in the manuscript. Also, the main study results might be of more interest to the national readers of Reunion Island. In all, the Methods section needs rewriting by addition of more explicit details from the study protocol before the review process could be continued any further.

Remarks on methodology:

1. A major issue is that CAP was not defined properly (only criteria of severe CAP were stated), and details were not given on how cases of CAP were ascertained. A brief summary of in-hospital algorithms should be added to the manuscript. Also, did all the patients receive the same diagnostic (eg. imaging) and microbiological studies before the final diagnosis of CAP was arrived at?

2. What is a cytobacteriological examination? This needs further explaining.

3. Did the patients have blood cultures taken?

4. Are all patients with severe CAP hospitalized at the ICU ward at Reunion Island?

5. How were eligible patients screened and included in the final cohort?

6. Was any patient follow-up seeked during the study period? If yes, how?

7. How was data collection executed? What was the data source? How were missing data handled?

8. The primary outcome should be defined by a hard clinical end-point, eg. in-hospital all-cause mortality at day-14 or alike. "Clinical and microbiological characteristics" are not endpoints – they are characteristics.

9. There is a contradiction in the description of statistical methods: an univariate pre-screening was done (line 133), but after that, only the "most clinically relevant factors" were entered into multivariate analysis (line 135)? This needs to be elaborated.

10. Adherence to the STROBE Statement is highly encouraged during rewriting.

11. I suggest using the term bronchoalveolar lavage instead of bronchoalveolar sputum.

12. I suggest that the term "adult patients" should be emphasized.

13. The name of the American Thoracic Society should be corrected.

**********

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Reviewer #1: No

Reviewer #2: No

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Submitted filename: PONE-D-21-05049 review.docx

Click here for additional data file.

4 Nov 2021

Nicolas Allou, MD August, 27th, 2021

CHU Félix Guyon

Réanimation Polyvalente

Allée des Topazes, 97400, Saint Denis, France

Phone: +2 62 90 56 94

Fax: +2 62 90 66 93

E-mail: nicolas.allou@hotmail.fr nicolas.allou@chu-reunion.fr

Dear Pr. Baochuan Lin,

Thank you for your letter concerning our manuscript entitled “Severe community-acquired pneumonia at Reunion Island: Epidemiological, clinical and microbiological characteristics, 2016-2018" (PONE-D-21-05049).

The comments were stimulating and challenging. We have therefore deeply modified the manuscript, taking all of the suggestions into account. Changes in the manuscript are in red font.

The manuscript has not and will not be offered elsewhere for possible publication, as long as it is under PLOS ONE consideration.

Ethics statement and consents from participants have been specified in the revised manuscript

We have added the data set of the study

We give a point-by-point response to the reviewers (see below)

We hope that these revisions have improved the manuscript.

Nicolas ALLOU, MD

COMMENTS TO AUTHOR:

Personally, I found the following points need to be clarified:

1. Prevalent pathogens for CAP are influenza, S. penumoniae. How does this compare to nosocomial pneumonia?

We have better redefined our diagnosis criteria for CAP in the material and methods section (lines 108-112).

2. CAP caused by influenza and S. penumoniae is year round, however, the authors indicated the rainfall play a role in the case of CAP. From the figure, it appears more case for influenza CAP in dry season. Any studies on influenza CAP related to the same phenomenon?

Several studies find an association between seasons and the occurrence of CAP and more particularly concerning influenza (Radina P, et al. Associations between seasonal influenza and meteorological parameters in Costa Rica, Honduras and Nicaragua. Geospat Health 2015 Nov 4;10(2):372/Oyelola A et al. Epidemiological analysis of association between lagged meteorological variables and pneumonia in wet-dry tropical North Australia, 2006-2016. J Expo Sci Environ Epidemiol 2020 May;30(3):448-458/ Julian W Tang, et al. Comparison of the incidence of influenza in relation to climate factors during 2000-2007 in five countries. J Med Virol 2010 Nov;82(11):1958-65/ Gwladys C, et al. Associations between meteorological parameters and influenza activity in a subtropical country: Case of five sentinel sites in Yaoundé-Cameroon. PLoS One 2017 Oct 31;12(10):e0186914/ Kramer SC. Development and validation of influenza forecasting for 64 temperate and tropical countries. . PLoS Comput Biol 2019 Feb 27;15(2):e1006742/Gentile A, et al. Influenza virus: 16 years' experience of clinical epidemiologic patterns and associated infection factors in hospitalized children in Argentina. PLoS One 2018 Mar 29;13(3):e0195135/Cilloniz C et al. Seasonality of pathogens causing community-acquired pneumonia. Respirology 2017 May;22(4):778-785). It has been added in the revised manuscript (lines 247-249)

3. The mortality rate is higher for influenza CAP, is this same from other region?

Mortality rate was higher for influenza CAP than for non-influenza CAP. The impact on mortality of the pathogen causing CAP is variable according to the studies. In Spain, Abelleira et al. found that CAP related to influenza A H1N1 had a poorer prognosis than non-influenza CAP (Abelleira R, Ruano-Ravina A, Lama A, Barbeito G, Toubes ME, Domínguez-Antelo C, González-Barcala FG, Rodríguez-Núñez N, Marcos PJ, Del Molino ML, Valdés L. Influenza A H1N1 Community-Acquired Pneumonia: Characteristics and Risk Factors-A Case-Control Study. Can Respir J 2019 Mar 17;2019:4301039. doi: 10.1155/2019/4301039. eCollection 2019) (Quah J, Jiang B, Tan PC, Siau C, Tan TY. Impact of microbial Aetiology on mortality in severe community-acquired pneumonia. BMC Infect Dis. 2018 Sep 4;18(1):451. doi: 10.1186/s12879-018-3366-4). It has been also found that mixed viral-bacterial infections may be associated with an increased risk of mortality (Quah J, Jiang B, Tan PC, Siau C, Tan TY. Impact of microbial Aetiology on mortality in severe community-acquired pneumonia. BMC Infect Dis. 2018 Sep 4;18(1):451. doi: 10.1186/s12879-018-3366-4)

It has been added in the revised manuscript (line 274-278).

Specific comments:

1. Line 54, 97 “All consecutive patients…” I am not sure consecutive is the right adj. to use. Suggest changing to “All patients…”

We agree with reviewer comment, it has been corrected in the revised manuscript.

2. Line 79 – 81, is there any CAP data in nearby area, Madagascar for example?

There are only few studies on CAP in the Indian Ocean region. There are only 2 studies concerning Madagascar but none concerning Mauritius or the Comoros archipelago (Razanajatovo NH, Guillebaud J, Harimanana A, Rajatonirina S, Ratsima EH, Andrianirina ZZ, Rakotoariniaina H, Andriatahina T, Orelle A, Ratovoson R, Irinantenaina J, Rakotonanahary DA, Ramparany L, Randrianirina F, Richard V, Heraud JM. Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013. PLoS One. 2018 Nov 21;13(11):e0205124. doi: 10.1371/journal.pone.0205124. eCollection 2018) (J L Rakotoson, J R Rakotomizao, A C F Andrianarisoa. Acute community acquired pneumonia: 96 cases in Madagascar . Med Trop (Mars) 2010 Feb;70(1):62-4).

It has been added in the revised manuscript (line 217).

3. Line 79, 81 &118, change “legionella” to “Legionella” since genus used alone should be capitalized and italicized.

We apologize, it has been corrected in the revised manuscript

4. Line 82,153, 194, 233 & 301,Streptococcus pneumonia should be “S. pneumoniae”

We apologize, it has been corrected in the revised manuscript

5. Line 116 – 117, change “Chlamydia pneumonia, Mycoplasma pneumonia, Legionella spp, Haemophilus influenza, Streptococcus pneumoniae and Bordetella (para) pertussis.” to “Chlamydia pneumoniae, Mycoplasma pneumoniae, Legionella spp, Haemophilus influenzae, S. pneumoniae, Bordetella pertussis, and B. prarpertussis.”

We apologize, it has been corrected in the revised manuscript

6. Line 142, please rephrase “…(incidence of 22 per 100,000 person- years)” for clarity. Did the author mean 22 per 100,000 person per year?

We agree with reviewer comment it has been modified in the revised manuscript

7. Line 154, Staphylococcus should be italicized.

8. Line 155, “Haemophilus influenza” should be “H. influenzae”

9. Line 155 – 156, “Legionella pneumophila” should be “L. pneumophila”

10. Table 3, “Haemophilus influenza” should be “Haemophilus influenzae”

We apologize, it has been corrected in the revised manuscript

11. Line 193 – 195, it is not clear about the correlation between rainfall and CAP, please expand the explanation.

We agree with reviewer comment. Several studies find an association between seasons and the occurrence of CAP but the physio-pathological explanation of this association remains to be established. This explanatory paragraph was removed because it was unclear

12. Line 200 – 206, maybe I missed something, I am not clear on the relevance of the risk factors for influenza with CAP? How about risk factor associated with S. pneumoniae or CAP in general?

We agree with reviewer comment, this analysis has been removed from the revised manuscript. Risk factors for developing CAP could not be assessed because there was no control group (without CAP).

13. Line 220 – 222, please clarify the relevance of this statement.

We agree with reviewer comment this section has been removed from the revised manuscript

14. Line 248, change “K. pneumoniae” to “Klebsiella pneumonia” since this is the first time Klebsiella was mentioned.

15. Line 274, Actinobacter should be italicized.

16. Line 285, “Staphylococcus aureus” should be “S. aureus”

We apologize, it has been corrected in the revised manuscript

Reviewer #1:

Thank you for sending me this manuscript for review. The investigators studied clinical and microbiological characteristics of patients with severe pneumonia who were admitted to the ICUs. The manuscript is of interest, however, several points need to be highlighted and revised as follow.

Abstract

Editing error: “causatives”

We agree with reviewer comment, it has been corrected in the revised manuscript.

Conclusions are not based on the results. Also, the recommendation of cephalosporin and oseltamivir needs revision to reflect the study findings and may lead to increased antimicrobial resistance.

We agree with reviewer comment, it has been corrected in the revised manuscript.

Introduction

Some general statements require evidence and to be specific, for example:

Initiate antibiotic therapy against all strains of S pneumonia and Legionella. This is a general statement that needs to be more specific on the empiric use of antimicrobials.

We agree with reviewer suggestion, it has been added in the revised manuscript

We agree with reviewer suggestion, it has been précised in the revised manuscript:i.e. a combination therapy with cephalosporin and macrolide or monotherapy with respiratory fluoroquinolone (83-85).

Methods

The study was conducted on ICU admitted patients, and they may not represent the study objectives rather than only severe cases that required ICU admission. So, study objectives need to be changed accordingly.

We agree with reviewer comment, it has been modified in the revised manuscript that it was all severe case of CAP hospitalized in ICU (line 91, 105).

It’s not clear too, how data were collected, was it a retrospective chart review?

It was a chart review of all patients hospitalized in ICU for severe CAP. It has been precized in the revised manuscript (line 104).

Statistical analysis

Line 5: First time mentioned abbreviation, the full name should be provided.

Also, the statement is not clear: “Risk factors of influenza PAC in bivariate analysis with P<0.1 were entered into a multivariate logistic regression analysis using backward selection with P <0.05”.

Has suggested by the Editor, the section on risk factors of Influenza CAP with multivariate analysis has been removed from the revised manuscript.

The reported incidence in the results section was different from the abstract and discussion, should be revised.

We apologize, it has been corrected in the revised manuscript

Table (1), abscess was mentioned, what does it refer to what type of abscess and which site?

It was pulmonary abscess, it has been added in the revised manuscript

Table (1), duration between symptoms and ICU admission, was it days?

It was days, it has been précised in the revised manuscript

Table (1), what does it mean of reporting the p-value as zero? (for influenza-like illness)

We apologize, this was an error, and these are P < 0.001. This has been corrected in the revised manuscript.

Table (1), how hazardous alcohol use was assessed, what definition was used, and how data were collected?

We have used The Alcohol Use Disorders Identification Test Consumption (AUDIT-C) with a with a threshold value of 4 for men and 3 for women (Bradley KA, DeBenedetti AF, Volk RJ, Williams EC, Frank D, Kivlahan DR. AUDIT-C as a brief screen for alcohol misuse in primary care. Alcohol Clin Exp Res 2007 Jul;31(7):1208-17. doi: 10.1111/j.1530-0277.2007.00403.x). It has been added in the revised manuscript.

Table (1), what does footnote 2 refer to?

It was a spelling error and it has been removed from the revised manuscript

Did the investigators collect any vaccination histories on influenza or pneumococcal vaccines among the study participants?

We apologize we dot not have this data

Table (3), footnote … “…. during flu cases” need revision.

What is “flu syndrome” mentioned in line 201?

We apologize during flu cases has been replaced by “Influenza CAP”. “Flu syndrome” was “Influenza-like illness” but it has been removed from the revised manuscript has it was in the multivariate analysis section.

Higher leukocyte counts mentioned in line 204 is not a risk for severe influenza as per the odds ratio presented.

We agree with reviewer comment. Moreover, it has been removed from the revised manuscript has it was in the multivariate analysis.

Line 212 need revision

We apologize, the line has been revised

Discussion

The second highest cause of mortality and years of life lost. Was there a difference between mortality and years of life lost?

We have deleted the second part of the sentence

in-ICU mortality in this study was lower than previously reported. Any specific reasons or contributing factors to be discussed?

It has been reported that mortality for CAP could reach 50% in patients hospitalized in ICU. Nevertheless, mortality in recent studies that evaluated severe CAP in-ICU patients was similar to that in our study: 22% in the study by Ferrer et al (Ferrer M, Travierso C, Cilloniz C, Gabarrus A, Ranzani OT, Polverino E, Liapikou A, Blasi F, Torres A. Severe community-acquired pneumonia: Characteristics and prognostic factors in ventilated and non-ventilated patients PLoS One 2018 Jan 25;13(1):e0191721. doi: 10.1371/journal.pone.0191721. eCollection 2018) and 27% in the study by Cavallazzi et al (Cavallazzi R, Furmanek S, Arnold FW, Beavin LA, Wunderink RG, Niederman MS, Ramirez JA. The Burden of Community-Acquired Pneumonia Requiring Admission to ICU in the United States. Chest 2020 Sep;158(3):1008-1016. doi: 10.1016/j.chest.2020.03.051. It has been added in the discussion of the revised manuscript (line 271-275)

Editing, line 253, “….. we find” should “found”

We apologize it has been corrected

What about the impact of empirical use of antimicrobials on the detection of organisms that have been reported in other reports.

The use of empirical antibiotics could theoretically have an impact on deep respiratory samples. But to our knowledge there is no study on the impact of one dose of antibiotic on the positivity of respiratory samples concerning CAP.

The investigators included a paragraph in the discussion about climate change and influenza types, although they didn’t provide a specific discussion or explored the relevance to the study.

We agree with reviewer suggestion, has also suggested by the Editor this section has been has been removed from the revised manuscript. Several studies find an association between seasons and the occurrence of CAP but the physio-pathological explanation of this association remains to be established. This explanatory paragraph was removed because it was unclear.

Conclusions should be revised to reflect the study findings.

We agree with reviewer suggestion, the conclusions have been modified.

Also, the recommendation of probabilistic antimicrobials and oseltamivir to every patient should be revised taking into consideration the potential risk for antimicrobial resistance and definition of severe pneumonia that may not be specific to be applicable in several care settings.

We agree with reviewer comment, we have removed from the revised manuscript the text concerning the treatment by oseltamivir.

Figure (2), worst survival was observed for cases with S pneumonia, this needs further discussion.

In the present study, the mortality rate in the subgroup of patients with S. pneumonia CAP was similar to that reported by Dupuis et al. They found that in-hospital mortality among the 1665 patients who required ICU admission for pneumococcal CAP was 22.8% on day 28 (Dupuis C , Sabra A, Patrier J, Chaize G, Saighi A, Féger C, Vainchtock A, Gaillat J, Timsit JF. Burden of pneumococcal pneumonia requiring ICU admission in France: 1-year prognosis, resources use, and costs. Crit Care 2021 Jan 10;25(1):24. doi: 10.1186/s13054-020-03442-z.). It has been added in the discussion section of the revised manuscript line 271-275).

Figure (1) (which is also written as figure (2)), about rainfall and influenza, showed three peaks of rainfall but not clear of an association with the occurrence of influenza or pneumococcal infection, more elaboration in this regard is required.

There is an association between the dry season and the occurrence of influenza CAP. This association was not found with S. pneumoniae. Several studies find an association between seasons and the occurrence of Influenza CAP but the physio-pathological explanation of this association remains to be established. This explanatory paragraph was removed because it was unclear.

Reviewer #2: Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical and microbiological characteristics, 2016-2018 (Manuscript No. PONE-D-21-05049)

In their manuscript, de Mangou et al. present valuable data derived from a retrospective cohort of patients admitted and diagnosed with severe CAP at Reunion Island between 2016 and 2018. However, significant scarcities of methodology detailed below could be identified in the manuscript. Also, the main study results might be of more interest to the national readers of Reunion Island. In all, the Methods section needs rewriting by addition of more explicit details from the study protocol before the review process could be continued any further.

Remarks on methodology:

1. A major issue is that CAP was not defined properly (only criteria of severe CAP were stated), and details were not given on how cases of CAP were ascertained. A brief summary of in-hospital algorithms should be added to the manuscript. Also, did all the patients receive the same diagnostic (eg. imaging) and microbiological studies before the final diagnosis of CAP was arrived at?

We have better redefined our diagnosis criteria for CAP in the material and methods section (line XX-XX). Data were collected using a chart review of all patients hospitalized in ICU for severe CAP. It has been also precized in the revised manuscript (108-112).

2. What is a cytobacteriological examination? This needs further explaining.

We apologize, the sentence has been reworded. Bacteriological examination of respiratory samples were always performed (sputum samples on non-intubated patients and tracheal or bronchoalveolar sputum on intubated patients (122).

3. Did the patients have blood cultures taken?

Yes, all patients had blood cultures. It has been précised in the revised manuscript (line 122).

4. Are all patients with severe CAP hospitalized at the ICU ward at Reunion Island?

It has been précised that it was all patients with severe CAP and hospitalized in ICU that have been evaluated. Indeed, some patients are not admitted to the intensive care unit because of ethical considerations

5. How were eligible patients screened and included in the final cohort?

We performed a retrospective chart review of all patients diagnosed with severe CAP. It has been précised in the revised manuscript (line 104).

6. Was any patient follow-up seeked during the study period? If yes, how?

Follow up was seeked during in-hospital hospitalization on chart patients

7. How was data collection executed? What was the data source? How were missing data handled?

Data collection was retrospectively collected on patient charts. And a column with the item missing data has been added in the tables.

8. The primary outcome should be defined by a hard clinical end-point, eg. in-hospital all-cause mortality at day-14 or alike. "Clinical and microbiological characteristics" are not endpoints – they are characteristics.

We agree with reviewer suggestion the primary outcome has been modified in the revised manuscript (line 137)

9. There is a contradiction in the description of statistical methods: an univariate pre-screening was done (line 133), but after that, only the "most clinically relevant factors" were entered into multivariate analysis (line 135)? This needs to be elaborated.

We agree with reviewer comment, has suggested by the editor but the multivariate analysis has been removed from the revised manuscript

10. Adherence to the STROBE Statement is highly encouraged during rewriting.

We agree with reviewer comment, adherence to the STROBE checklist has been checked in the revised manuscript (missing data in tables…) and a statement has been added (101).

11. I suggest using the term bronchoalveolar lavage instead of bronchoalveolar sputum.

We apologize, it has been corrected in the revised manuscript

12. I suggest that the term "adult patients" should be emphasized.

We agree with reviewer comment, it has been specified in the revised manuscript (104)

13. The name of the American Thoracic Society should be corrected.

We apologize, it has been corrected in the

Submitted filename: Response to Reviewers.docx.doc

Click here for additional data file.

4 Jan 2022

18 Jan 2022

Nicolas Allou, MD January, 14th, 2022

CHU Félix Guyon

Réanimation Polyvalente

Allée des Topazes, 97400, Saint Denis, France

Phone: +2 62 90 56 94

Fax: +2 62 90 66 93

E-mail: nicolas.allou@hotmail.fr nicolas.allou@chu-reunion.fr

Dear Pr. Baochuan Lin,

Thank you for your letter concerning our manuscript entitled “Severe community-acquired pneumonia at Reunion Island: Epidemiological, clinical and microbiological characteristics, 2016-2018" (PONE-D-21-05049R1).

The comments were stimulating and challenging. We have therefore deeply modified the manuscript, taking all of the suggestions into account. Changes in the manuscript are in red font.

The manuscript has not and will not be offered elsewhere for possible publication, as long as it is under PLOS ONE consideration.

All relevant data are within the manuscript and its Supporting Information files

Ethics statement and consents from participants have been specified in the revised manuscript

The authors received no specific funding for this work.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

We give a point-by-point response to the reviewers (see below)

We hope that these revisions have improved the manuscript.

Nicolas ALLOU, MD

COMMENTS TO AUTHOR:

Reviewer #1: Thank you for revising your manuscript. However, there are some points that I think need a revision.

1. Conclusion in the abstract and at end of the manuscript that melioidosis and Acinetobacter app should be considered in patients returning from Madagascar, this conclusion is based on only a few number of cases and shouldn't be generalized especially an adjusted regression analysis was not performed.

We agree with reviewer comment, it has been deleted from the conclusion of the revised manuscript (line 68).

2. In the Materials and methods, the investigators mentioned that written information notice about the process of data collection was obtained, but they didn't report about severely ill patients and those on ventilators or not fully conscious, how that process was complete.

We have clarified that in the revised manuscript. Information notice about the process of data collection was obtained from their legally authorized representative in case of patients unable to obtain the information (line 99).

3. In the Material and methods, third paragraph: a reference on the CAP clinical definition is required.

We agree with reviewer comment, it has been added in the revised manuscript line 110).

4. In the results section: The acute physiology score was first mentioned with no explanation of its definition, components, or reference. The same was in Table1 for CURB-65.

We agree with reviewer comment, references have been added in the revised manuscript (Lim WS, van der Eerden MM, Laing R, et al. (2003). "Defining community acquired pneumonia severity on presentation to hospital: an international derivation and validation study"/ A New Simplified Acute Physiology Score (SAPS II) Based on a European/North American Multicenter Study. JAMA. 1993).

5. Table 2: Biological characteristics should be changed into laboratory findings.

We apologize, it has been corrected in the revised manuscript

6. Discussion should highlight that severity of influenza-CAP may be associated with patients' underlying conditions not directly related to the influenza infection itself compared to other infections. This can be evidenced if a multivariate regression was performed.

We agree with reviewer comment. We found that patients in the group with influenza CAP had higher mortality rate than patients with non-influenza CAP following univariate analysis. Nevertheless, patients with influenza CAP had more frequent comorbidities (age over 65 years old, asthma, diabetes mellitus…) and there is no multivariate analysis performed. It has been added in the revised manuscript (line 275).

7. Kruskal-Walis test was mentioned in the statistical analysis, although not shown or used in the results.

We agree with reviewer comment. It has been deleted from the revised manuscript.

Reviewer #2: In their revised manuscript, de Mangou et al. addressed all the methodological remarks. A reconsideration of publication could be recommended.

Specific comments:

1. Line 78 – 80: This statement needs reference(s).

We agree with reviewer comment. References have been added in the revised manuscript

Microbial Etiology of Pneumonia: Epidemiology, Diagnosis and Resistance Patterns. Cilloniz et al. 2016

But clearly, it can’t be generalized because there are differences between causative organisms encountered in the tropics compared with temperate climates. Due to both environmental and socio- economic factors, diseases such as melioidosis, leptospirosis and tuberculosis are more widespread in the tropics. For example, observation of the aetiologies of community-acquired pneumonia (CAP) in an Asian outpatient setting showed that the most common isolates were Chlamydophila pneumoniae, followed by Mycoplasma pneumoniae and Streptococcus pneumoniae. Lim_et_al-2018-Respirology_pneumonia in the tropics.

2. Line 83 & 163 : Change “S. pneumonia” to “S. pneumoniae”, “H. influenza” to “H. influenzae”.

We apologize, it has been corrected in the revised manuscript

3. Line 100: this statement needs further clarification.

We agree with reviewer comment, it has been clarified in the revised manuscript (line 98).

4. Line 122 – 124: Needed to specify the methodology used? Culture or other methods?

We agree with reviewer comment it has been specified in the revised manuscript that identification was performed with Gram staining followed by culturing with definite microorganism identification. Alternatively, identification was performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

5. Line 252: Change “Acinetobacter” to “Acinetobacter”.

We apologize, it has been corrected in the revised manuscript

6. Discussion: Use either oseltamivir or Oseltamivir: Be consistent.

We apologize, it has been corrected in the revised manuscript

Submitted filename: Response to reviewer_R2.docx

Click here for additional data file.

9 Feb 2022

2. Line 83, change i.e.a to i.e. a

3. Line 96, change N° to No.

4. Line 98, delete "about the process of data collection"

5. Line 265, change S. pneumonia to S. pneumoniae

6. Line 276, change "...diabetes mellitus…" to "...diabetes mellitus, etc."

23 Mar 2022

Nicolas Allou, MD March, 22th, 2022

CHU Félix Guyon

Réanimation Polyvalente

Allée des Topazes, 97400, Saint Denis, France

Phone: +2 62 90 56 94

Fax: +2 62 90 66 93

E-mail: nicolas.allou@hotmail.fr nicolas.allou@chu-reunion.fr

Dear Pr. Baochuan Lin,

Thank you for your letter concerning our manuscript entitled “Severe community-acquired pneumonia at Reunion Island: Epidemiological, clinical and microbiological characteristics, 2016-2018" (PONE-D-21-05049R2).

As recommended, the manuscript has been revised by an English translator specialized in medical English (Ariane Dorval) and has been greatly improved. Changes in the manuscript are in red font.

The manuscript has not and will not be offered elsewhere for possible publication, as long as it is under PLOS ONE consideration.

All relevant data are within the manuscript and its Supporting Information files

Ethics statement and consents from participants have been specified in the revised manuscript

The authors received no specific funding for this work.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

We give a point-by-point response to the reviewers (see below)

We hope that these revisions have improved the manuscript.

Nicolas ALLOU, MD

Submitted filename: response_reviewer_R3.docx

Click here for additional data file.

5 Apr 2022

Severe community-acquired pneumonia in Reunion Island:

Epidemiological, clinical and microbiological characteristics, 2016-2018

PONE-D-21-05049R3

Dear Dr. Allou,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication once you correct the following:   Line 55: delete "consecutive", line 78" suggest changing from "they recommend" to "the recommendations are", and line 273, italicize   "S. aureus" to " S. aureus ',  and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Baochuan Lin, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

7 Apr 2022

PONE-D-21-05049R3

Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical, and microbiological characteristics, 2016-2018

Dear Dr. Allou:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Baochuan Lin

Academic Editor

PLOS ONE